Software. Software. Software! Process. Process. Process!

At each step of the process you have entries being made by different people into a software system. Discrepancies surface rather quickly. For example, if you buy 10 pounds of beef, and only sell 20 1/4 pound hamburgers before you run out, there's a problem!!!

You will not be able to eliminate all possible theft. Managers at each location should be empowered to make decisions. They should be trusted people. And as the saying goes: "trust but verify", so spot check often.