That's about how my chaos is. 114/E10 parts goes like brakes, interior, exterior(?), fuel, instrumet (gauges), suspension, steering, ignition, electrical (wiring, relays etc), lighting and so on. Same with E21 & E30 parts. Engine parts goes between M10 & S14 boxes with some separation like head, bottom end, oil pans, starters etc. Hoses are in same boxes (expect S14). Race parts goes like engine, springs, shocks, brakes & misc. And yes there are those general stuff boxes too but i like to have them as few as possible. There are like a hundred or so boxes (15x23x12" WxLxH) + other parts that dont fit in them so... uhm...
... but somehow i usually manage to find what i'm looking for.
Keep em like how it makes some sense to you then you'll automatically search from the right box. Quite many times it helps if they are sorted by chassis and labelled by year & model.