A VERY easy way to do this is to make sure you have full electric gel and a fully upgraded chemical thrower before entering the elevator to the final boss.
As soon as you stab Atlas and he punches you away, hold down that trigger and spray away with the electric gel as it leaves him unable to move and he just stands there taking it.
When he jumps back in to recharge, reload your gel and stab him again.
Repeat until he dies.
There is JUST enough ammo to kill him, I think I ended up with less than 10 or so units left
On hard, I went through just one or two med packs as I took no damage from atlas
himself, just bots and splicers that I completely ignored.