Smoke is the boss counter. For the big gunner going up the building it's smoke, shoot, smoke, advance while shooting. This usually gets him in 2-3 shots unless he sees you. The knife guy in the basement won't heal if he can't see you. Shield guy sometimes dies in 1 shot if he can't see you even from the front (requires the armor piercing perk). If you're lucky he'll throw a molotov when you drop in, which drops his shield allowing a 1 shot with killing spree up.

Doing the basement last is faster even with the backtrack from the right side of the screen because getting back up is painfully slow.