Thank you for taking the time to post a reply here in the Community, @AtoZ123. I'm here to help you.
 

If you want to manually record the bank deposits in QuickBooks Online, you can follow the process below:
 

Step 1. Put transactions you need to combine into your Deposited or Undeposited Funds account. 
Step 2. Combine transactions in QuickBooks with a bank deposit.
Step 3. Include bank or processing fees.
Here's how:

1. Scroll down to the Add funds to this deposit section.
2. Enter the fee as a line item.
3. Select who the fee was from (ex: the bank charging you).
4. Select Bank Charges from the Account ▼ dropdown.
5. Enter the amount fee as a negative number. For example, if the fee was GBP £ 50, enter –50.
6. Review the deposit total with the bank fee.
7. Select Save and close or Save and new.

For further reference, you can check this link: Record and make bank deposits in QuickBooks Online.
 

If you want to automatically pay the invoice to QuickBooks Online, I suggest calling the Zettle app support.
 

Here's how to contact the Developer Support:
 

1. Go to Apps.intuit.com.
2. Type in the Zettle app in the search bar.
3. Select the Contact tab or the Support tab.

If you need further assistance, don't hesitate to post a reply. The Community and I are willing to assist you. Take care and have a wonderful day ahead!