You need to have a very tight system of controls on your cash management from the time it leaves the customers hand. Look for excessive numbers of no sales or voids. If you have a physical check that gets rung in, consider randomly checking the total dollar amount of the checks to the amounts rung in. Make sure that you have separated the duty of writing a check and ringing in cash payment. That should be enough to at least get you thinking if not get you started.
Cash is one of the easiest things to steal.
I run a gourmet deli in Baltimore and have experienced similar concerns with my cashiers regarding cash handling. You only work on your own cash. Cash deposits are counted daily by two different people in a management position, it is reconciled with a daily cash report printed from the computer system. If you go over that amount it is documented. After the third time you receive discipline up to and including termination if it continues.