I try to prep the body first before assembling any other part of the car. If it is a multi-part body (bumpers, etc) I glue those on and clean up the seams. Part of the body prep is getting rid of mold seams ans sink marks. After all the sanding and putty is finished up, then the first primer coat goes on.
I personally feel that painting any part of the body while on the sprue is a waste of time, since you will have to clean up the attachment points anyway, then re-primer.
After a dceade of practice, I think that I'm pretty good at painting car bodies, but I've got a long way to go.
I learned a lot from Alex Kustov. He's got some great tutorials on his website: www.italianhorses.net.