I'm in a similar situation about the kinds of wood pieces I keep for later use. One thing I find helpful is that I have a box for small (24" or less long) leftover pieces of each species I use a lot (cherry, curly maple, walnut, African mahogany) and boxes for the different fretboard woods. For fretboards I like the large flattish boxes that Stew-Mac ships things in. I've been lucky enough to have outside-the-shop storage for my large piles of unused lumber, but when I move next year I'll have to consolidate. One thing that might be worth looking into is building a small shed in the yard for wood storage, unless your shop is more climate-controlled. Around here most towns let you build up to a 144 square foot shed without a permit, or even an 8x8 would be enough to store a lot of lumber.