OK, I am honestly not a very organized person. But the one area that I can say IS organized is my tupperware cabinet, probably more organized than anyone I know and it stays that way.
My first suggestion is to use your smallest cabinet for tupperware. It's just one of those things that will expand to fit any space you give it. Mine is super narrow.
Second, it really really helps if you have all of one kind of plastic storageware (tupperware, rubbermaid, snaplock, gladware, whatever) Two kinds at the most. Just because everything will nest better if you don't have 5 different brands. And just recycle those used sour cream containers.
I put the largest containers and odd-shaped containers on the top shelf. with their lids underneath them. On the second shelf I have a little wire shelf to give me extra room (meant to hold dinner plates I think). I put a nest of containers on top and the lids for them underneath. To the side of the wire rack I put a different shape of lid.
On the bottom shelf I put the ones I used most often.
When nesting tupperware, most people will try to just stack from biggest to smallest, which is logical but will not work. If you have 2 bowls the same diameter that nest, but one is deeper than the other, the deeper bowl goes on top not on bottom! Try it both ways - putting the deeper bowl on top will make the stack much shorter.
Anyway, I just got new tupperware myself, but with my old rubbermaid set, the square bowls were on the wire rack with square lids underneath and round lids to the side. The bottom shelf held rectangle containers with lids on one side of the stack and round bowls on the other side.