It's always tempting to take a pretty box, save it and put sewing supplies in it. That's the way you get 5 boxes with thread and you only look at one.
Take your supplies out and group them by type- needles, pins, scissors, thread, buttons, etc. This gives you an idea of how much you currently have of everything. Then go to Walmart (I like their prices for plastic storage) and purchase however many boxes you need per catagory. I find that buying the same box for all makes for neater storage.
One important thing to buy is a flat plastic box with a lid of about 8x11 or so, around $3.00 for your UFO or the current project you're working on. Put your pieces in the box and work from it. That way, at day's end, you pile all the pieces back in, put the cover on and put it away.
Find an inexpensive bookcase on which to stack all your boxes and resist the idea of cluttering it up...if you work with a system like this, it will make it easy to find your stuff and easy to keep it clean.