Hello, @accounts212.

You can receive the payments for each invoice. Just make sure to choose Undeposited Funds from the Deposit To drop-down. Let me guide you on how to do it.

1. Go to the +New icon.
2. Select the Receive payment.
3. Enter the details of the payment.
4. Select an appropriate payment method.
5. To complete the transaction, click the Save or Save and new button.

Once completed, you'll need to group the payments so that they'll show as one deposit on the register. Make sure to indicate in the deposit the fees that were deducted from it.

1. Go to the +New icon.
2. Select Bank Deposit.
3. In the Payments section, put a check-mark next to the payments that you want to group.
4. From the Add funds to this deposit section, enter the amount of the total processing fees.
5. Make sure to enter the amount with a negative sign to denote an expense.
6. Review the details of the deposit to ensure that its total matches with the joint payments.
7. Click Save and Close or Save and New.
   

You can refer to this article for detailed steps:  How to link a deposit to an invoice.

Also, I've got these to help you tracking, categorizing, and splitting invoice payments in QuickBooks:

• Download, match, and categorize your bank transactions in QuickBooks Online
• Find missing payments you want to deposit in the Bank Deposit window 

Let me know if you have other questions about managing your invoice payments in QuickBooks. I'm always here to help.