I've spent a stupid amount of time shopping for storage for my sharpening gear. I originally used a Plano 3 tray tackle box. It worked fairly well, but most of the tray compartments are too small for most of the things I use. Too shallow for bottles of oil. Too narrow and too short for decent sized stones. I stored all the big stuff in the bottom of the box, which worked ok, but not great.
When I upgraded to a set of three 8" DMT diasharp plates, they wouldn't fit and I went shopping for a bigger tackle box, or a tool box. I didn't really find anything I liked; mostly too big and with too few compartments. I finally settled on this box from Sears that's worked out quite well:
Sears 18" Cantilever Box
All of the trays you see, both top and bottom, are removable. The ones you leave in place, lock in place with the lid shut, via some grooves in the lids and landings on the bases of the box. I've arranged mine to hold everything I want, reasonably separately. Highly recommended, though it *does* get heavy with those DMT plates in it.
When I got waterstones I wanted something to store them in too. Maybe something like what I had, but with nice big compartments for those monster waterstones! I spent hours going to every craft supply place in town, including sewing supply shops. There are a LOT of boxes available for crafting, but none that I found that would fit waterstones and hold them the way I wanted. So I did what HwangJino did: I bought (on sale at Target) a sort of giant (15 quart) hefty "tub", see through, with a lockable lid. I soak the stones in it when I want to use them, and then put them back in dry. If I'm going to transport the stones, I stuff towels between them. I use the towels for cleaning knives and cleaning up water when I sharpen, so they do double duty.
I'd still like something more compartmentalized, but it's fine for now. I sometimes think I'm crazy the way I approach this hobby. Then I come here and realize: Yeah, I'm crazy, but at least I have company!
Brian.