Yeah I've been thinking about separating starting units as well. For now I've utilized tiny plastic totes I found at Office Max (about the size of your palm). They fit in the insert too. I have one for free people tokens and dice, one for all the shadow tokens and dice, and one for fate tokens. The FP + characters and shadow + Bolg are in their own quart ziplocs. All the decks of cards are wrapped with rubber bands.
Ideally, I want to get a tiny felt or cloth draw-string bag for Fate tokens. I am not totally satisfied mixing my recruitment tokens with leadership tokens, wrath tokens, etc. I'm using tiny jewelry bags I got at the Container Store (essentially little zip-loc bags ranging from the size of your thumb to the size of your entire hand) for the neutral components like damage tokens and dice. I might start using them for some of the player tokens as well since it's still a hassle to pick through them all, particularly with mustering tokens and Beorn's wrath tokens.
I've been thinking of having a bag of starting units for each player to go on the board and having the rest separated out into their own baggies.
I think once I am more familiar with how the units and recruitment tokens go out setup will be a lot quicker anyway.