This is probably one of those things where you get 5 people together and end up with 6 opinions, but here is how we did the last one. A piece of 1/2" thick plywood laying across the aprons and bolted down as the fenders would if they were there. It stuck out about 6 inches over on each side, and was away from the firewall several inches also. The fenders were then bolted through the plywood in a couple spots with washers smaller than those on normal fender washers. This way we could get the fender lips. The hood sat on the plywood and was pulled forward a bit so we could get the cowl "lip" also. Headlight buckets and quarter panel extensions were bolted to the car, but I added spacers so that there were gaps. Everything was in position related to the final resting places. We had a side panel for vents, parking lights, bumper guards, etc. so they would be vertical, and a side table for hood vents so they could be painted when flat.
Doors and deck lid painted on the car first - so all jambs were taken care of.
A couple of pics included. Hood and some other things were already removed at this point.