How I did it.
The process Rick described will work fine, especially with the added tip by RVG8tor.
What I did: I fit the cowl with the upper skin all cleco'ed, and the baggage skin not cut out of the upper skin - just as RVG8tor says.
Then, I waited to do the baggage door until the upper skin was fully riveted on. Probably didn't need to, but it seemed the most sure thing.
To fit the latch blocks once everything is done, I put some double-sided tape on the proper spots in the fuselage, strapped the baggage door closed, climbed inside, slid the latch blocks into about the right place and had an assistant turn the lock, pushing the pin into the latch block and seating the latch block into the double-sided tape. Repeat for the other block. Then, when the door is opened, the blocks are held in the right spot for match-drilling and screws.
I may have lucked out -- I didn't need to tweak the block position by elongating any screw holes, but you could if you needed to.
Good luck, take your time. It is one of the most difficult spots on the airplane to get a truly professional looking job of it, and unfortunately it is also one of the most conspicuous.