I know it's a big thread, but it really has everything you'll want to know...
http://www.therpf.com/showthread.php?t=87056
Just a few quick tips:
I use both Pepakura Viewer and Designer. Designer for resizing, Viewer for quickly and easily figuring out which parts are next on whatever section I'm cutting/gluing.
I prefer to score and cut out as I go. It's easier to keep a stack of paper neat rather than a bunch of cut out parts.
I use a blue ball point pen to score mountain folds (evenly dotted line) and a red pen for valley folds (dotted/dashed line). The color doesn't matter, it's just nice to have two different ones and not black, since those are your cut lines. Score and fold EVERY line, even if it looks like it's not going to bend much in the final position. Also cut every line, even if it basically attaches back to itself. These are generally relief cuts that let the paper bend around compound curves and wonky stuff can happen if you don't. There are a lot of lumpy Iron Mans out there...
I use Elmer's glue because it holds fast, isn't messy, and is cheap. Hot glue is messy and hot, but some people like it. Super glue is messy and impossible to reposition, but some people like that as well.
When it comes time for the first coat of fiberglass resin, I mix in a splash of acetone to help it soak in.
Rather than fiberglass mat, I prefer polyester (polar) fleece because it's cheap ($3/yard), doesn't get hairs everywhere, and you generally only have to use one layer. I sometimes do two layers if it's a big surface. Again I mix acetone with the resin so it soaks quickly all the way through the fleece. I find it's easier to dip the fleece to soak it rather than trying to brush the resin on.
Acetone also extends the cure time, so rather than having to rush (especially if it's hot out), you get plenty of time and then some.
But, there are a dozen different ways to do each step, so you should find what works best for you.
-Rog