I do same a sculpin_c and Brian, just put labels on the lid over each compartment with hook size, type and some time manufacture. I have three 18 and a 12 compartment for hooks and another six 18 compartment ones for beads.
With regards to labelling the hooks; I don’t. I only use a select range of shapes, some are manufacturer specific such as the Partridge klinkhåmer 15BN or Fulling Mill Czech nymph and ultimate dry, but many are a particular shape or style but could be from any brand. Keeping a small range limits possible confusion for me and any really weird hooks are just kept in their packets.