Thanks for reaching out to us in the Community space. I can help you subtract an expense from a bank deposit.
When making a deposit, you can add a new line with a negative amount under Add funds to this deposit.
Go to the Plus icon.
Under Other, select Bank Deposit.
In the Add funds to this deposit section, enter information about any additional items to include in this deposit, including who the item was Received From, the Account, Payment Method, and Amount of the item.
Add a new line for an expense transaction and enter a negative amount.
This information should help you deduct an expense from a bank deposit. I'll be on the lookout for your reply and to further assisting you if you have other questions. Wishing you and your business continued success.