Set it up so that the lid can be used as a base for the pedal board while you're playing. You'll need to ensure a couple of things:
- that the lid is strong enough to handle "missteps"; and
- that the lid doesn't slip in either position (i.e., the lid holds its place against the frame of the pedal board through some sort of joint - maybe a lip).
If you do this, you may find that the best shape for everything is shallow rectangular at the sides for the pedal board casing, and somewhat wedge-shaped for the lid, with the wide end covering the pedals in transit, flipping around the rear while playing to raise the back a bit and angle the board towards you. If you do this, add some rubber feet on the lid.
A & B show (very roughly) closed and open. (The black thingie in B is meant to be a pedal.) C is a cross-section through the sides of the lid and case to show the kind of join I mean. You should only need fasteners to hold it closed in transit.
Doing it this way means you don't have to find a place to put the lid in cramped quarters. If that isn't a consideration, Dr Mayhem's suggestion definitely has the virtue of simplicity.