Since I don't know your situation, I'm not sure if this would work for you, but I use individual student trays for math, art and science.
They are fast food plastic trays. I have organizing charts for pattern blocks, counters, etc.
that way, I can see at a glance whether or not the children have all the counters or small pieces that they started with. It works well for accountability.
Here's a link in case you want to see what I'm talking about.
http://www.equippers.com/Trays-Fast-Food/6373.asp
I like the 10 x 14 trays.