I've settled on three-section boxes for each named block. I use two-section boxes for the annual core sets (e.g., M13 and M14 in the same box). This has really simplified things for me, as an entire block rotates out each fall (along with one core set).
That's what I've been doing with everything in the past few years (after going from single boxes to those giant five row boxes, to some other formats and things between).
For my older cards (where I do not have playsets of every block), I simply alphabetize everything in a set of two-channel boxes. Since I use Deckbox to help with deckbuilding, I don't need to sort those cards by color to browse what I have. If I want to see the cards, I just use the spoiler view. Once I know which cards I need for a deck, I open the box, go to that section of the alphabet, and find what I need.
The only exceptions to this basic system are non-basic lands and planeswalkers. Those I keep in a holiday gift box so they are more convenient to find, and to make them quickly portable.
One tip I have for making dividers is to use rule cards topped with post-it style tab dividers. You can get a pack of 36 of them for under $3 (less when on clearance), and they work perfectly. I always have plenty of rules cards around, and I can always grab more tab dividers at nearly any store on the continent.
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TradelistBlack and Blue--not just for bruises anymore.