Mary Harbolt knows how to manage student manipulatives. She teaches a 4th/5th blend at Faubion Elementary in Portland, Oregon, and wrote in with this fabulous idea...
I have a marble system in my classroom. [Students work together to earn--and sometimes lose--marbles that can earn them special privileges and/or rewards.]
If a math manipulative hits the floor and I pick it up, it's my marble. If a student picks it up first, no marble is lost. This system makes the students hypervigilant. At the end, if all manipulatives are put away, they get a marble.