What I currently do is have 5 wheatley fly boxes and 2 cf design fly boxes. The CF designs get used for bass flies, they're deep and accommodate big poppers.
The 6" wheatleys are setup 1 for streamers, 1 for nymphs/wets/worms/eggs, 1 for dries, 1 for terrestrials and a 4" for tiny dries and nymphs on threaders. I usually end up with 3 or 4 boxes on the water. Sometimes I do mix a few patterns in each. But they're divided up for the most part.
Everything else goes into one of these from Plano:
It holds 4 separate plano boxes inside. Can easily grab the whole thing and throw it in the car.