Thanks for taking the time to share your experience, QED.

I'll give details about the process and the solution that you can use. When you sync your Square app with QuickBooks Online, transactions are automatically downloaded as invoices or payments.

If you want to record an invoice in QuickBooks Online, then you'll want to do the following:

• Create a receive payment once your customer paid the invoice. 
• Deposit the payment and include the processing fees.
• Match the deposit to the Square transaction downloaded in the Banking page.

To create a receive payment for the invoice entered in QuickBooks, make sure to deposit the amount to the Undeposited Funds account.

Here's how:

1. Go to + New > Receive Payment.
2. From the Customer drop-down, choose the customer's name.
3. Select the Payment date, Payment method, and choose Undeposited Funds account from the Deposit to drop-down list.
4. Under the Outstanding Transactions section, put a check mark on the invoice you want to pay.
5. Click Save and close.

Once done, let's record a bank deposit to include any processing fees by following these steps:

1. Go to + New > Bank Deposit.
2. Select the bank account where you want to deposit the money.
3. In the Select the payments included in this deposit section, put a check mark on the payment you want to deposit.
4. Under Add funds to this deposit, select the customer's name from the Received From column.
5. Select an expense account from the Account column, and enter the fee as a negative amount.
6. Click Save and close.

Finally, match the deposit to the payment posted in the Banking page. 

Here are the steps:

1. On the left panel, click Banking.
2. Go to the For review tab.
3. Find the square payment, and click the Match link. 

Please see these sample screenshots for a visual guide:

I'm adding these articles for reference:

• Sync Square with QuickBooks Online
• Record invoice payments in QuickBooks Online
• Record and make Bank Deposits in QuickBooks Online
• Categorize and match online bank transactions in QuickBooks Online

When you're ready to reconcile the account, you can find the instructions here: Reconcile an account in QuickBooks Online.

Should you have more questions about Sync Square with QuickBooks Online or recording the transactions, please let me know. I'm just a few clicks away to help you some more.