For organization when running the game, I usually use 2 inexpensive plastic desk drawer organizers to hold all the bits and pieces, something similar to
this. With the organizers, I can separate the gold pieces by value, and the monster standies by size (tiny, small, more-or-less human size, and huge) etc., before the game. During the game, it's very easy to simply grab what I need from the correct pile, like extra movement or health tokens, ransacked counters, etc. Hope this helps!