Maybe you need an excel sheet to keep track of Lot numbers? I just store everything in my office, but they are small.
So I have a big plastic tub for all of my wine charms. This is more than enough room to where they only take up about half of the bin. I like it because when it comes time to do a craft fair, I can put the remaining items in the bin and still have room for business cards and other table extras.
My cake toppers are all in a one of those gallon zip lock bags, with the exception of my parasols, which most are already made up and packed in boxes ready to ship. Some of my bigger order listings are made-to-order so I have the supplies on hand in a plastic drawer (one of those stack-able drawers) where I keep all my paper supplies together.
My jewelry is wrapped individually because of the sterling silver (tarnishes if you leave it out in the open air), which I recycled the plastic poly bags I get my beads in to store the bracelets once they are finished. The larger necklaces are stored in larger poly bags, I just save all the ones I get from my jewelry supplier. They all are in my cabinet, which I have this one from Ikea with various doors and drawers to keep all of my art/craft supplies:
http://www.ikea.com/us/en/catalog/products/70201811/#/80193740(I have it in white, and have various black and white inserts to hide my supplies)
These bags are easily put in my bin for shows, so everything is pretty much wrapped up and stored away from my cats, since I know there are those with allergies out there.
Depending on how big your items are, you could store them in a bin, or those plastic bins with the drawers you can find at Target and Walmart, which are great for organizing.
If they are small items like beads, you could label them with the lot # and organize the small packs by number in order, where you have rows labeled (i.e. Row 1: 0001-1000, Row 2: 1001-2000, etc), like a card catalog system, along with having a spreadsheet to keep it all straight.