I have always covered the pieces separately, and then hinged them. What I think would be the best way, is to cover the hidden areas first, install the hinges and attach the surfaces, then cover the remaining areas. What this buys you is complete coverage, smooth operating hinged surfaces, and most importantly, if using CA hinges, no CA dribbled all over the finished monokote. If I am using hinge points, I definitely do all the covering before assembly.