Very old unanswered thread, but wanted to comment.
Making your own decals is great. I'm not quite sure what you meant on what to do if you use decals, so this is what I'm thinking about. For exterior decals, clean the body and stick them on where you want them. I would not do anything beyond that IMO. Now if you made decals to use to help spray designs into the paint on the inside (you did paint the inside, right?), then lay them on thinking in reverse. The first coat you put down is your base layer. Once it's down, you can't paint anything over it to show on the outside. You have to plan your design in reverse and have all stencils and decals down before you spray or at least covered so you can lay them on a clear area to pain again. This can be extremely frustrating when you make the simplest of mistakes and get an order wrong, been there!
It's been years since I painted one of my own bodies, and the only one that I have left was from either an Associated TC3 or a Losi XXXs that I ran inside on concrete. And that has been well over a decade ago!