Hello! I should inform you that for future questions like these, refer to the stickies at the top of the page labeled "HELP! For XXXX", in this case you would post in "HELP! For Pepakura". This helps veterans find and answer questions quickly, since many do not really look through the noob threads beyond those stickies.
To your question now, though, it's a tricky thing and you have to figure out what works best for you. In theory you could leave one flap open and let the resin do its thing.
What I like to do is find the flap that is most important to closing off the other ones, it's usually the longest edge, as you need to get your fingers in to get the others. Then I bend up the flaps so they prefer to stick up rather than down, hose them down with glue (I use PVA glue), and hold it closed. It won't seal it super well, but it gets the job done until it comes time for resin.
You can also try only half gluing that last flap closed, that lets you reach in to hold the pieces together, and still gets it as closed as possible, another reason to use the longest edge as the last step.
The last idea is as follows... When you seal off a piece, you won't be able to harden it so that it can withstand handling (just pepakura, or just pepakura+resin will not be able to take handling), so you can just plan ahead and cut a hole in a large face. Then use that hole to glue all the edges together, since those are the important parts. Once it comes time to harden the piece, you use that cut hole as your funnel to pour the rondo/whatever inside the piece! Kill two birds with one stone, since you'll have to cut that hole anyways. (Sealing the hole off is another step altogether.)
