Well, the answer to what goes in which pocket has already been posted.
Everything that goes in my pockets has a snap attached to it -- either a boltsnap or a double ender. I use double-enders, of course, on spools, but also on my backup mask (because if you deploy a mask, it is irritating to have a snap attached to it). The snaps are clipped into loops of cord (I don't use bungie).
How you tie the cord or bungie IS important -- Danny Riordan didn't like the way I had done it, when I took Cave 1, because I had tied the cord in a big circle that meant some of it was on the outside of the pocket. (Imagine you are sitting and looking at the pocket from the top -- pass the cord through the grommet and tie it in a knot. You now have a loop, part of which is IN the pocket, but part of which is outside.) He told me things would migrate out of the pocket and catch on line. I thought he was nit-picking, until the second or third time a snap caught on the line because it was sticking out of my pocket. Then I retied them.
The new way is to tie a knot in the end of the cord. Pass the cord through the grommet so that the knot is on the outside. NOW tie a knot in the cord, making a loop that is entirely within the pocket, and such that the inside knot keeps the cord from sliding out through the grommet. Now stuff will stay inside.
If you are carrying a lot of small things (as with GI3's pocket contents) it can be useful to put a loop in the front and back grommets, and separate the things so that, when you pull up one loop, you only pull up some of the pocket items. For example, I keep my car key on the rear loop, because it is something I am NEVER going to need during a dive, and I'd just as soon it never came out of the pocket and risked being lost.