When updrilling, you typically want the wing supported flat on the table so you can make adjustments to verify it is level and square (no twist.)
Once everything is updrilled and deburred the holes themselves should keep everything square, so you might find the top and bottom skins easier to rivet by standing the wing vertically on sawhorses, forward edge down.
http://www.rynoth.com/wordpress/waiex/2 ... ompletion/Regardless of the method, just be sure when you cleco then flip the wing that you properly support it. i.e. do not rest the wing on the tips of the clecos.
edit: also, if I recall correctly, the bottom skin is placed and drilled first. Can't remember if that was in the plan instructions or not but I seem to remember it from the builder workshop and it's the order I did (bottom>top>front.) Might be because it lays flatter than the top skin and helps lock the wing into place before flipping it.