If you bring the right tools (and you probably will), this fight becomes a piece of cake, even on Hard difficulty.
Before you enter the fight, make sure you have a full supply of Electric Gel and a fully upgraded Chemical Thrower. After you stab Atlas and he throws you across the room, hold down the fire button and spray him with the Electric Gel. When he goes off for a recharge, reload the Thrower, stab him again and repeat the process until dead.
You may run out of ammo before you can kill him. It shouldn't be a problem (unless you're an awful shot) as Atlas will be near the point of death. In this case, just hit him with whatever weapons you have.