Aligned, stiff and matched from side to side -- if one is stiffer than the other you'll get a bit of roll every time you turn. Don't hesitate to throw away one or both of the flaps that came with the kit.
I vastly prefer pinned hinges. Put in at least four hinges: I think the Sig Twister plans call out three on a side. I was given a plane that had six on each flap, and it worked just fine.
Make sure that the center lines of all the hinges and the pivot for the flap horn are all aligned. If you don't get this right the flaps will tend to spring to some preferred location. Also make sure that everything is free. The worse the misalignment, the worse it'll happen. I generally cut the slots for my flaps when the plane is still in bare wood, then test the fit by putting them together dry. You should be able to assemble the flaps with the horn and everything and have them flop down under their own weight in both directions (wing upright and inverted). If there's friction or spring, figure out what the problem is and fix it.
If you glue everything in solid, do it after the plane is fully covered but before paint. My preference is to make the flaps removable by replacing the hinge pins with one length of music wire, and putting a brass tube in the flap to receive the flap horn, but that's probably too much work for your first flapped plane. After you glue the hinges in check for friction again.