The most expensive parts are the NXT or EV brick, the motors, sensors and batteries, so these need to be monitored closely.
Use a permanent marker or sticker to number each group's main parts. Keep them in a seperate tub with the same number.
Ideally these parts should be kept in a locked cupboard.
Before each project make sure each group has all their main parts.
All the other bits and pieces can be stored in a separate big tub. Tip all these parts on a blanket or sheet at the start of a lesson, then it will be easy to pack up at the end.