I always cut out and drill my bodies before painting them. It ensures they are alligned properly and doesn't scrape the paint if you hit it with scissors.
I line up my body and mark with a sharpie where to drill when clear.
If there is paint already on the body and I still need to drill holes, I put a dab of grease on top of each of the body posts and lower the body onto the posts as straight as possible. Just ream where the grease is.