I use a dedicated minis case.
Don't know who makes it, but it runs between $40 and $50 US depending on where you get it.
If I describe it, you'll know what I am talking about the moment you see it, so here goes:
It's big and black.
2 small pockets in the front with velcro closures (great for dice, pens, pencils, erasers, etc)
1 large, zipper pocket just behind the small ones,
and the BIG zipper pocket for holding the minis.
Carry strap.
Inside the Big pocket are soft, foam, well, Boards, I guess you can call them. About an inch and a half thick, 8 inches wide and a little over a foot long.
The great thing about them is that, while the edges and bottoms are pretty solid, the main part of the foam is already cut most of the way through -- Perforated, if you will -- into little squares about a quarter inch to a side and an inch deep. So you can easily and quickly remove just enough of those pieces to fit whatever you want to fit into that slot.
Makes it possible to carry you ACTA fleets (lots of ships), your CBT models (I have 3 companies in the first 4 layers), and still have room for a couple more things...
It really is worth the money and you have to see it to understand why I sing its praises so much. Wish I could remember the maker...