Personally i use 1/2" drywall on top of my building table. Its cheap and pins hold well into it. Many people i know use hard foam boards or ceiling tiles. I also use reynolds wax paper on top of plans, again theres other things but its what i find easy for me. They sell plan protectors perhaps Great planes makes it. The brand eludes me atm.

you definitly should lay out the wing on the plans before gluing for just the reason you mentioned. If any alterations need to be made its a Pain and risk breaking the delicate balsa [:@]
I always use a square to keep them vertical to the building surface before gluing them in.