I've tried all kinds of stuff and all sizes of boxes. I can never settle on just what works every time.
However, for the last year or so I have been the 3600 size boxes and have a box for 1 oz and 3/4, a box for 1/2 oz, a box for 3/8 oz and a box for 1/4, 3/16, and 1/8 oz.
That way all I have to do if pick up the box for the size of jig I want to throw then look for the color combo I want. I try to keep 4-6 of each color that I carry in the boxes and take along an emergency bag that is kept in the truck, just in case.
As for trailers, when I get done with a jig I drop it on the deck. When I am back home and the jig is good and dry, I'll remove the trailer and put the jig back in its box if it isn't damaged. The trailer I normally deep six. I don't put trailers back in jig boxes due to moisture and salt.