I've been there, done that! A few years ago, I bought several new slit foam boxes and decided to start over. I gave some thought as to how to organize my boxes and even made row by row diagrams of how I intended to populate them. I think the key for me was to think hard about what flies I was really using. I now carry fewer patterns, but more flies of each pattern. Basically I carry ...
-- Medium size box with all purpose nymphs eg, scuds, PTs, HEs, Princes
-- Medium size box with midge and mayfly adults. These are organized by our local hatches -- eg, BWOs, Hendrocksons, Sulphurs.
-- Medium size box with caddis and terrestials
I carry the first two boxes all year and add the third in April or so. I don't carry a streamer box, but I have a small selection of streamers on a foam drying pad in my pack

Of course, it hasn't stayed quite that simple. I've added a small box specifically for tricos which I carry during trico season. I've also added a box of large mayfly drakes -- nymphs and adults -- which I carry at times and in places where I expect to run into them. I also have a number of boxes at home which serve as "warehouses" for resupplying my boxes.

Another concept that might be worth considering is carrying what a friend of mine calls a "turtle box". This is the box where he keeps the experimental flies , swap flies, and such that haven't earned his confidence.