A quick heads up, I'm not a pro with atlas, I play him well but that's mostly it, so don't expect this guide to be perfect, it is based off of my understanding of the character and the game. If you like this guide, please upvote it. I put a lot of time, effort and study on this guide, it reflects all I've learned on these months playing Atlas in ranked and casuals. With that out of the way, let me give you some tips.
1) Use setback(RMB) only when crucial, that is when you see an enemy that is low and is escaping, a killable enemy going around the corner(if using the talent Deja Vu), or to escape enemies when you don't have your Stasis Field(q) or your Second Chance(f). If you use it too often, enemies will get resilience and counter your ult and you Set Back, but if you don't they won't find it necessary to buy resilience.
2) A few good uses of your ult are: ulting on the enemy support to kill the tanks, or the support and tanks to kill the dps; ulting so you can stagger the death of an enemy champion; ulting so enemies won't be able to get to the point in time to get overtime(usually when 80% point capture above without comeback mechanic)
3) Something I see a lot of Atlas players do is ulting on someone, ulting them again when the effect of the ult stops and then using the Setback on them so they get "stunned" for about 10 seconds. I wont say that is so bad, but it isn't something I'd recommend. What you gotta remember is that the enemy won't take dmg for those seconds, and the long duration of the "stun" makes people usually insta buy resilience.
4) If you dont have 2 of your cooldowns or more, just wait for them to come back, don't flank anyone without two or more of your cooldowns.
5) Atlas is an off tank. DO NOT IN ANY CASE USE ATLAS AS A MID TANK(unless in casuals, because you don't usually have two tanks). Try and flank a lot with atlas, go with a flanker if you have one and put pressure on the backline or kill one of the dps or support.
6) Dealing poke damage with Atlas is also good when you can't get in the enemy backline.
7) When you shoot, there's some time until you can use your abilities again, so keep that in mind when you think you might get into a risky position or situation in which you might need to use your cooldowns.
8) Atlas' gun is one of the hardest weapons to use in the game, if you've just started playing Atlas, practice controlling the recoil and knowing when to shoot and at what mode.
Deja vu: I use Deja vu as my talent because I think it is easier to hit targets with Setback and you can hit them around the corner. Even though some people say that Temporal Divide is the better talent, there's a reason why I don't think it is so good. Your Stasis Field only lasts 5 seconds and the cooldown doesn't start until those 5 seconds end. Your Stasis Field has a 14 second cooldown, but with Temporal Divide that becomes almost 30 SECONDS. That means that you're only gonna use it once every minute if you use it immediately after the Stasis Field is off cooldown. Not only that but Temporal Divide can be countered very easily. If you're playing against a Temporal Divide Atlas, whenever he uses his Stasis Field just give the enemy team some space, you must not take any fights with someone behind the Stasis Field. Whenever Stasis Field ends, tanks make space and you're free to take any fights you want again. Atlas and his team need to be behind the Stasis Field to get any value, if you move ahead of it so they won't be behind it, you completely negated his talent and the 28 second cooldown.
Beyond The Veil 5: This card is very good for retreating and for and when you wanna rush and hold W against your enemy. When retreating, look back and throw your Stasis Field right in front of you and go through it, your enemy isn't going to be able to shoot you and you will run away without much effort. When rushing by yourself,(cause you don't usually have that much teamwork to set up an attack as a team) make sure to have your Second Chance ready in case things go wrong. Go through the shield and rush up to a support or a dps, try and get one of them down, if you're still above 3000 hp go try and get a second backline champion down, right after use your Second Chance and get back with your team. If they focus you too much before or after the first pick don't try to get a trade, use Second Chance right away because you've already put enough pressure or the backline and the enemy team probably retreated.
Old Wounds 4: Atlas has very small hp, so boosting that number up is good.
Continuum Shift 3: Going back and getting a bit more health is always good and pairs up well with the rushing style of Beyond The Veil 5.
Paradox 2: The cooldown for Second Chance is very big, lowering that is a good idea.
Hell Hunter 1: Hit a shot, don't waste ammo, why the hell not?! Jokes aside, this is a very solid one point card that lets Atlas deal more poke damage and not reload so much.
Setback becomes a lobbed explosive, capable of Rewinding multiple enemies.
Beyond The Veil
Passing through Stasis Field increases your allies' or your own Movement Speed by 35% for 3s.
Increase your maximum Health by 600.
Second Chance sends you 1.2000000000000002s further into the past.
Reduce the Cooldown of Second Chance by 1s.
Generate 1 Ammo after hitting a fully-charged weapon shot.
Your weapon shots reduce the effect of healing on your target by 75% for 1.5s.
Receive 15% more healing from other players.
Cauterize 3 is a must pick against literally any support or character that has any kind of self sustain. You're gonna be dealing a lot of damage and trying to confirm kills, and without cauterize that task becomes incredibly difficult. Rejuvenate is a bit less mandatory to get it up to a level 3, because you're gonna be in the enemy backline a lot and it's going to be difficult for your support to heal you, but when you aren't in the enemy backline and you're poking with your team, rejuvenate is going to be useful. If your team has a Jenos, be sure to get rejuvenate up to a 3 because Jenos can heal without being close or having line of sight, and if the jenos is decent, he should know Atlas is a good target for his marks because of the high damage output he has, specially with the mark.
Reduce the duration and effectiveness of Crowd Control and Slows by 20%.
Reduce the Damage you take from Area of Effect attacks by 7%.
Reduce the Damage you take from Direct attacks by 7%.
Increase the range at which you see nearby stealthed targets by 15 units.
Your weapon attacks deal 20% increased Damage to Shields.
Your weapon shots deal 20% increased Damage to Deployables, Pets, and Illusions.
Increase your Mount Speed by 15%.
These items depends on what the enemy team has and how the match is going. Only do these items before the ones listed above if it's necessary.
Resilience: if the enemy team has a CC heavy composition.
Blast Shields: If there's a AoE character or ability giving you trouble.
Haven: If there's a direct damage ability or champion giving you trouble.
Illuminate: If flanking a sha lin, strix, or if there's a skye giving you trouble.
Wrecker: I rarely recommend wrecker since Atlas isn't usually gonna be in your backline instead of the enemies' shooting shields, just recommend it in case going against Torvald or Khan.
Bulldozer: It's good against Imani dragons, Luna, Inaras using the cripple talent, or Bariks using Architectonics.
Master Riding: This one just depends on the map you're playing in, if it's a very long map which whichever team gets to point or flank route faster gets advantage, then Master Riding 1 or 2 is definitely recommended
Reduce the Cooldown of all your abilities by 10%.
If you're done Cauterize and Rejuvenate 3 and you feel like you don't need any of the situational items or already finished one of them, getting Chronos would definitely help. Atlas' cooldowns are huge, so getting as much Chronos as you can is gonna help you. Just do the first two items, check if you need any of the situational ones, and if you don't or already got them up to a 3 or as much as you feel is necessary.
Some of the champions are here for the same reason, so I'll put them together.
Torvald, Fernando, and Vivian: Setback can cancel or remove the shields from all of these characters(Torvald's personal shield can only be removed if he lost all of it and put it back with his F ability). With Vivian and Fernando, don't shoot the Setback into the shield or it'll not work, so shoot the Setback behind them or (against Vivian specifically) on her feet.
Ruckus: Ruckus also gets countered by the fact that Atlas can negate the usage of his shield, but the reason I put him separate of the others is because Ruckus' ult is also countered by the fact Stasis Field can block all of it. But be careful against good Ruckus players, they'll wait until you use your Stasis Field to ult, so when you think Ruckus has an ult, stay close to your team and don't use your Stasis Field until he ults.
Furia and Grover: Both of them have an ability that gives a high amount of healing with a big cooldown(when furia is using the talent Solar Blessing). That means that Atlas can negate all or most of the healing they give using Setback. Grover's ult is also countered by Atlas' Setback.
Drogoz: Atlas can hit Drogoz in the air very easily and deal a lot of damage due to his hitscan weapon that doesn't have much falloff. Atlas is also rarely hitten by Drogoz ult and Spitfire+Salvo combo. When Drogoz ults, you can either use Behind The Veil 5 to run away from him or use your Second Chance when he's close to hitting you with the ult.
Ying: Ying's ult is completely negated by Atlas ult and Setback.
Damage Pip: The card that nearly all Damage Pip players put in their loadouts, Moxie, can be negated by Setback.
Heal Pip: Mega potion has a high burst of damage with a kind of high cooldown depending on the loadout the player is using, and that is countered by Setback.
Honestly, Atlas isn't weak against any champions, he has little soft counters which I'll talk about below.
Jenos: Jenos is nearly unflankable by most champions, and atlas isn't any different. Finding where Jenos stays is already hard enough because of how safe Jenos players usually play, killing him is also harder than it should be because of his Q ability and his high mobility.
Seris: Seris isn't quite a soft counter to Atlas. The only problem is the heal she gives is not counterable by Setback. Even though Seris has a high amount of healing just like Grover and Furia, her heals are have a low cooldown, so as soon as your ally is full healed and Atlas uses Setback, Seris will have another heal ready, but Cauterize can still affect her healing.
Evie: Evie is also just a pain in the backside against all of the champions when you know how to play her. Since Atlas' shots have a some time to get fully charged,(it will usually not be worth it to use the non-fully charged shots against evie unless she is right in front of you, which I find unlikely to happen) Evie can dodge all of his shots or Ice Block so she won't be hit by them. The same happens to you Setback when using Deja Vu since it has a little drop off.
Terminus: Terminus does something similar to Evie but less effective. Terminus can block all your fully charged shots and your Setback with ease, but, since Terminus has to be right in front of anyone to deal damage to them, Atlas can shoot without charging it fully. Terminus players can learn that as the match goes and try to block it with his Siphon, so try missing some on purpose to bait his siphon and then you can shoot or shoot your Setback while the Siphon is in a 2 second cooldown.
Khan: Khan can pressure Atlas fairly well as long as you don't have your Stasis Field. As soon as you use your Second Chance to get your health back he's probably gonna ult you if he has an ult, so the best you can do is try not to take so much damage by fighting behind your Stasis Field or try and get help from one of your teammates. Khan can also block your Setback and your ult, something you can do against that is trying to bait him by looking away when ulting or when preparing a Setback then looking back at him and shooting it as soon as you can so he won't block it. If you're close to him and you are using Deja Vu, you can look at your feet and throw the Setback and he probably won't expect it.
These champions can be weak and strong against Atlas depending on their legendaries.
Inara: If using Mother's Grace, Inara can be really strong against Atlas if she knows how to use her RMB when Atlas uses his. Otherwise, Inara is hard countered by Atlas. Her RMB is the best ability in her kit, and with it comes 30% of extra healing from allies while her RMB is activated. That is now fully countered by Atlas ult and Setback.
Makoa: If Makoa is using Leviathan, he's neutral against Atlas. Otherwise, he's very weak against Atlas. His ult is completely negated by Atlas ult and Setback when without Leviathan. When you see a Makoa that is not using Leviathan when you are playing Atlas, is the only time I'd recommend using the 10 second "stun combo" that I talked about in the beginning but just when Makoa ults.
Io: Just haven't tested enough against her.