There's a quick way to make sure you've received the correct amount of cash from your drawers.
This report lists the daily totals for each store for Cash, Check, and Credit Card. To quickly check that you have received the correct amount from your store check that your daily total matches the total amount you received from all drawers at the store in question. If the numbers are within a few dollars or your accepted difference range then you're set. If there's a discrepancy then you need to look a bit closer using the cash box report.
2. Under reports select "Cash Box" and select the day in question from the calendar. Look at the drawers for the store that had the mismatch.
Use the ending totals and the list of payments to figure out what caused the discrepancy. If the discrepancy is exactly the amount of the payments it's possible the employee never received the cash but accidentally marked the order paid. Sometimes you'll need to look at the opening amount of the following day to find the missing money. One common cause is that the drawer started short so the employee topped off the drawer with cash from the day's payments. But then that begs the question "why was the drawer short?". You can check the closing and opening balances of a drawer from day to day to make sure there isn't anything being stolen in between shift changes.
If you still can't figure out what happened to the missing money ask the employees if they remember anything and don't be afraid to show them this ledger. If they know that every transaction is logged they'll be less likely to even think about stealing.