I just read Iron Man Rapture and I can't really figure out how it fits into continuity. Is it before or after Iron Man dissasembled? How did they bring Tony back to life at the end?

It's a "What If?" story. Marvel has just been labeling books strangely of late. A case in point being "Young Avengers" just being called "Avengers: Children's Crusade". Although it would help sales as some collect only Young and are fearful of being dragged into the rest of the franchise crossovers.

I forget if the logo was on there, but also anything marked Marvel Knights these days are pretty much standalone tales not linked to anything. Mostly to feed the trade paperback market for the casual reader so they don't feel lost, or that they have to get some missing volume.

It was marked Marvel Knights, and I was trying to figure out what this had to do with Black Cat, Iron Fist, etc