You can wrap the bolt heads with a single wrap of masking tape, and use a 6 point socket or wrench instead of a 12 point.......less chance it will mar the bolts. I think I have seen sockets that are lined with plastic or something to protect the bolts, but I can't remember where. If they do get scratched, a small artists brush with some of the same automotive paint you originally used can be applied to the boogered up areas, and will blend in pretty well.

Don