While you decide which system works best for you, the instructions below will help you re-assign the payments in the meantime: Everything you could ever need to know about Syncing with Square can be found in our guide at the included link. The suggested method is to invoice and process the payments in Square and then import the sales data, or use QuickBooks for the entire process instead. This seems to be in line with the rest of the discussion here, as the option for invoicing with QuickBooks but processing the payment with Square is unavailable at this time. To make sure I understand you correctly, is the Square App importing a duplicate invoice in addition to the one that you create and send directly from QuickBooks? If that's the case, these duplicates will overstate your income. Hello and welcome to the Community, here to help you find the remedy you're looking for. You would need to manually apply an additional payment for the fee to each invoice. I tried this and it works and tracks but takes more time than just doing a manual deposit. Either the invoice will show the fee as unpaid (in which case you can record an additional payment in the aomount of the fee for the invoice as a 'square service charge expense 'account to clear it). There is no way to have this automatically happen. That way square will show the invoice as paid (example $100 charge and $100 square payment) and the bank deposit will also match (example $100 charge, $100 less $2.00 fee recorded on bank deposit = $98.00 deposit which matches the bank deposit) At the time of the credit card deposit to the bank, I simply choose the deposit(s )that are reflected in the deposit, then add another line to the deposit using 'square service charge ' (expense account) and a negative amount equal to the actual deposit dollar amount sent to my bank. The money is then in my 'undeposited funds' account. I solved this by not having Square do the automatic bank deposit.
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