Greetings, @pipes-plumber.

You can record the invoice payment in full and deposit it to the Undeposited Funds account. From there, use a bank deposit to deduct the commission amount paid to SumUp.

Here’s how:

1. Click the + New button and choose Receive payment. 
2. Select a customer from the drop-down.
3. Pick a Credit Card as a Payment method and choose Undeposited Funds as your Deposit to account.
4. Mark the invoice you wish to pay.
5. Hit Save and close.

Check out this article for more details: Record invoice payments in QuickBooks Online.

Once done, create a bank deposit. Enter the commission taken as a negative amount. Follow these steps:

1. From the + New button, choose Bank deposit.
2. Pick an account where you wish to deposit the funds to.
3. In the Select the payments included in this deposit section, select the checkbox next to the payment.
4. Go to the Add funds to this deposit section and choose the posting account of the commission.
5. Under the Amount column, enter the commission money as a negative value.
6. Hit Save and close.

I’m adding this article as your reference: Record and make Bank Deposits in QuickBooks Online.

Know that you're always welcome to drop by the Community if you need anything else. I'm right here and ready to help. Have a nice day!