Hey Neuras- unopened charm packs get stored in my precuts drawer as is.
Once they've been opened any leftover charms get mixed in with other leftovers and the ones that I cut myself from scraps. I store these in stacks in a shallow drawer separated as follows:
1. Solids and prints that read as solids
2. Prints
3. Batiks
Each of these stacks are sorted by value with darks on the bottom, mediums in middle and lights on top. Works pretty well for me, I can just lift the stacks out of the drawer and quickly pull out what I need for a project.
Rob