Basically when I purchase packaged supplies I'll use Avery removable Print-n-Write labels to record right on the package what price I paid, the date, and a little code that represents where I purchased it, then put the packages up on peg board. Once the package is opened (or for loose purchased items) I use 4"x6" zipper top baggies. I put the little label on the outside of the package and inside I include a 3"x5" index card where I record the total number of pieces (or inchs) for the purchase price, how many pieces I've taken to use on which project, and if there were any damaged/unusable pieces. All of these go into 1 of those 12"x12"x4" scrap book crafting containers. For most beads I organize by color and seperated by glass, stone, Swarovski, and other inside the individual storage case. Each metal has it's own case regards of what the products is, and that I seperate by finding, bead, and other.
When I'm working on a piece I'll keep the entire package or baggie from each supply together in a different smaller storage box about the size of a basic bead board. Inside the small box I include a regular sheet of paper to write down any design specs or ideas as well as the list of "ingrediants and the supply price. This way if I'm side tracked and need to put the project aside I can return to it later and have notes on what I was planning to do and what the cost of supplies used already on the piece.