I deal with two types of APIs. Well-documented and otherwise. For well-documented APIs, I can simply re-read the documentation to figure out the other side of my code.
For the rest of it, I try to write as cleanly as possible, and as robustly as possible the first time, so I'm not in the dark the next time I have to look at it. If I have to take time out to re-understand how it works, I'll just take the time and not feel guilty about it. The company wanted me to use that dreck, I'm not going to feel bad about having to take more time with it.
I don't think comments would help much in the second situation given decent engineering the first time around. If it's my code, I'll usually recall the idiocy I had to work around when running down whatever issue had me looking at it again.
For the rest of it, I try to write as cleanly as possible, and as robustly as possible the first time, so I'm not in the dark the next time I have to look at it. If I have to take time out to re-understand how it works, I'll just take the time and not feel guilty about it. The company wanted me to use that dreck, I'm not going to feel bad about having to take more time with it.
I don't think comments would help much in the second situation given decent engineering the first time around. If it's my code, I'll usually recall the idiocy I had to work around when running down whatever issue had me looking at it again.