I started out doing just the front fenders on my car. Then I did the hood, then the body of the car. Now in the winter, I am working on doing other body parts. I am using Rustoleum, and I don't see any issues doing it however it makes sense for you. I am however going to wait until I have the whole car put back together to do the final wet sanding, that seemed to make the most sense for me, so that I get everything looking the same when it is done.

Hope this helps.

Gerbs