I have recently taken the books over for a very small coffee shop. It is a hot mess. Their bank account is constantly being overdrawn because of mismanagement. They have been paying expenses out of the cash sales, like payroll and everyday expenses. The sales are being recorded but they aren't being deposited. Basically the only thing being deposited are the credit card sales for the most part.How would I go about recording these in Quick books, since the money never hit the bank? I have created a petty cash account in quickbooks as well as a cash drawer. I am still confused on how I would record the cash because it was never deposited?

The reason the bank account is over drawn is not because the deposits are not made, it is because someone writes more checks than money deposits.

To answer your question regarding allocation you need to create a bank account and a cash account as a bank account and record the transactions paid in cash and received in cash as if they had been paid from the bank account. This will enable you to record the sales as well as the payments. Should cash be deposited in the bank account you can handle this as a transfer if it isn't specific to a days sales. As far as the overdrawn account is concerned you need to convince the owner to handle matters in a more normal manner of banking the days takings and perhaps using a credit card to make payments if insufficient funds are in the bank account. Once you get a handle on all transactions I expect you will find the business is somewhat marginal