I totally stink at re-packaging, unless I am going on a trip when I need a compact tying set - in which case I seem to fit the entire mess into a small carry-on box! Go figure. Stand back when I open it though - poof!
Here's my logic:
I have three of said Iris rolling drawer units, one for steelhead, stripers, and trout. Within these drawers the big drawers on the bottom contain tupperware and stuff, the smaller ones on top contain dubbing, packaged stuff, etc.
I do not maintain individually separated packages once they're opened. I bundle in themes.
First, the fly type (above). Then the material purpose - so for steelhead hardware, tinsels and flosses, hackles, wings collars and throats, etc. The head cement stays with the tools (bodkins, scissors, vise, etc).
For stripers: hooks, eyes, tools stay together. Hackles stay together. Chenilles and ez-body (stuff that wraps the hook shank) stays together. Then lots of body/wing material make up the striper kit for the most part.
Here's an original trick for keeping synthetics in order: Buy a $3 clear flourescent bulb sheath at Home Depot. Cut it so it's longer than the ultrahair strands. When you're done with the synthetics, group them together by the stapled-end and insert into the tube. You'll need enough to make a snug fit. Now knock the tube on the table or something until the material slides into the tube. Perfectly straight for the next tying session. Works for flashabou, sparkleflash, ultrahair, superhair, angelhair, anyhair that's synthetic.
If you don't take that advice and have krinkled up synthetic hair, just use a hair dryer on warm and brush it to straighten it out. Takes about ten seconds, don't let it get too hot of course. Wasy as pie.
Everyone probably already knows the trick of steaming natural feathers to straighten them out so I won't bother.
For not synthetics I use freezer wt ziplocs and big tupperware tubs to sort out marabou, rabbit strips, hackles, dubbings, wing materials (mallard, turkey, fox, squirrel, swan, pheasant, etc). Within each of these categories everything is fair game, meaning that I will put every conceivable color of marabou into the marabou bag/bin/container, etc.
I do not individually package and mark anything, just not that detailed although I envy those who are.
The other best thing I've done is buy the handy dandy two-shelf hobby box, also from Iris. One might think I have stock in them, hmmmm not a bad idea. It's about the size of a medium large tackle box and has two interlocking shelves with a very accomodating lid system that puts up with all kinds of abusive over packing. They thought enough to leave a gap between the edge of the shelf and one of the ends so that tall epoxy bottles like devcon fit perfectly in the end, even if you keep them in the box the two parts come in. I then cut the clear light sheaths to fit in the bottom under the trays, which hold all the hooks and tools you could dream of - all in one portable kit.
I have three of those to match the three tying themes of steelhead, striper and trout. I never filled the trout box so my wife claimed it as her sewing box, and she won't give it back.
On occasion I will package by pattern - in other words all the stuff I need for sedge muddlers, pupa flies, black bunny rats, etc - in the same ziploc bag just to make it easier to tie on the airplane