Since you do not have undeposited funds during the month in QB, you cannot use the “Make Deposit” in QB to record the real deposits. This is the recommended procedure:

  1. Make the deposit in the bank and save the deposits receipts
  2. Use the “Payment Detail” report to go against the bank receipts during the month
  3. Import the IIF file at the end of the month
  4. Use “Make Deposit” in QB to go against undeposited funds

See Also
Quickbooks - Can I use Account numbers?
Why is my QuickBooks IIF file showing a negative balance?