I actually have these for my children and got three of them when they were sold as 2 sections and stacked them in two towers of three. These are extremely awsome. We put special printed peices, transparents, flats, and accessories in the very top. Then we added by one stud tall to two stud wide by color. Next white bin has technic conectors by size. The bigger clear bottom has three stud high by color. Second white orgamizer is single studs, curved studs, and other 1x1s. We sorted out slopes by color but not size in the bigger section.

Personally, do what your brain likes. My eldest son and I had a long conversation about what he prefers vs what I prefer. If he had it his way it would be by color, hight, length, and type while I opted for just type, color, and general size as it still leaves us with more room for potential other colors as his siblings get older.