Hi there, @fcharlip and @kmwolter,
Welcome to the QuickBooks Community. I’m happy to help resolve the double sales and duplicate deposits when synching transactions from Bigcommerce and Braintree.
When merchant deposits are automatically imported from the bank, you’ll need to match them with the existing invoice/payments in the program. Only adding them will create new sales in QBO, which can cause discrepancies with income.
Here’s how:
1. Go to the Banking tab.
2. Pick the account from the Bank and Credit Cards drop-down option.
3. Locate and click the downloaded transactions, one at a time.
4. Hit Find match.
5. Set Show to All and enter the From and To dates.
6. Choose the invoice or payment to match.
7. Click Save.
You can find more information about how QuickBooks Online handles and analyzes the data from the bank in the Add and match downloaded banking transactions article.
With regard to the Braintree deposits without the fees, we can add new deposits. Let me walk you through the steps:
1. Click the Create (+) menu.
2. Choose Bank Deposit.
3. Pick the bank.
4. In the Add funds to this deposit, select the expense account you use for tracking bank fees.
5. Enter the fee as a negative amount.
6. Hit Save and close.
To learn more about this process, you can check out the Enter a bank service fee while using a third –party merchant service article.
That’s it. You can run the Profit and Loss report to ensure your income and expenses are correct.
I’ll be here if you need help with anything concerning QuickBooks. Wishing you continued success.
