After the body is smooth then it is ready to apply the undercoats prior to painting. The goal is to smooth out the wood grain and to provide a surface for the paint to stick to.
First up is a lacquer sanding sealer. I brushed on 8 coats of sanding sealer, lightly sanding after each application. Basically, you keep putting this stuff on until you don't see any wood grain texture. You can still see the grain but you want to check the texture. This is a critical step. You don't want your guitar body to be all rough like an unfinished piece of plywood.
After the body looked good I moved on to primer. I used Duplicolor Filler Primer that I picked up at an auto parts store. Again, I used lacquer, since I planned on using the Duplicolor lacquers for the paint and gloss coat. Everything has to be compatible so it can all stick together.
Anyway, I put on so many coats that I used up the whole can of primer. Once the guitar turned gray I could see a few spots where wood grain was showing through. I just sanded through those and put on some sealer until it was good. For small grains I just gave it an extra blast of primer.