A good way to handle it would be to buy a few big compartment tool box things (sorry I cant think of a correct name or better descriptor
), or just get some other sort of storage unit. We have several mindstorm kits in the same class room, each in their own box, and then we divided them up into the compartments by common parts, like gears, 1x4 bricks, motors, senors, etc. You can probably do a few different things depending on how specific you want to get in keeping the stuff apart, like gears in general or specific sizes of gears.