Happy to have you here on the Community page, @y_dunlop.
Let me share the detailed steps so you'll be to record the invoice payment and the fee accordingly.
First, you have to record a Receive Payment and deposit it to the Undeposited funds.
- Select Receive payment under Customers from the +(New) icon.
- On the Receive Payment page, select a customer name under the Customer section.
- Look for the invoice you want to pay under the Outstanding Transactions section.
- Enter the payment amount under the Amount received section and choose Undeposited Funds under Deposit to.
- Save the transaction.
Once completed deposit the amount, then add the PayPal fee as a negative amount under the Add funds to this deposit section.
- From the +(New) icon, select Bank deposit under Other.
- Pick an account where you want to deposit the amount under the Account section.
- Locate the payment under Select the payments included in this deposit section, then mark the box beside it.
- Go to the Add funds to this deposit section, then select the account for the fee and enter a negative amount under the Amount column.
- Click on the Save and close button to record the transaction.
Get back to me if you have any other questions. I'm always here to help. Have a good day!