To organize them I used the dividers that came with the box, and labeled them SCA, Klingon, Fort 1846, Ren Fair, and a few others. I sorted my fabric by what period costume I was going to make out of it. It doesn't matter as long as they are grouped in an order that makes sense to you. If nothing else sort them by color. Now that you have them done.
Patterns have to be the hardest things to deal with.
They tear, they lose pieces, and they never cooperate. I have found that the best way of dealing with them is to prep them before you need them. When I start the planning for a costume and will be using a particular pattern. I will open it, and cut out each and every piece in the largest size. Then I iron them and refold them and place the pieces, the instructions and the cover in a quart sized zip lock bag.