Yes, the money went into your bank account, but what did you post it to in QuickBooks?  The transaction journal should show you a Debit to your bank account and Credit to whatever account you posted it to when you created the deposit.  If it is a Deposit/down payment from a customer, it should have gone to a liability account (because you have money you haven't earned yet and you have a liability to perform a service or deliver a product).  You then need to zero out that liability account when you deduct the deposit/down payment from an invoice.  This is where the Deposit box won't let you debit that liability account.