Hey Torbeck,
I have an alternative option, you'll have to go into your historical transactions and change them, but i know this works on QBO.
Use the Undeposited Funds account to it's full potential here. Mark your Daily Sales Receipt as "Undeposited Funds" in place of your bank account. Record an Expense for the commision, also using "Undeposited Funds" instead of your bank account.
You deposit the remaining in your bank account - When you have done this you can create a new Bank Deposit, and you should be able to Select the Sales Receipt, and Select the Expense - Giving you an overall amount you're depositing matching what is in the bank statement. As long as the date on the bank deposit you've created matches the transaction hitting your bank account, you should find an immediate Match to the Deposit.
Let me know if that helps you.
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