OK.

I think I've now got this working and showing the transaction on the PayPal Bank feed.

!! IMPORTANT !! - Ensure the date payment is received and the dates of the deposits ect all MATCH.

1. On the invoice, click the Receive Payment button.
2. Select the correct invoice on the Receive Payment screen.
3. In the Deposit to field, choose Undeposited Funds.
4. Click Save and close. 

Then

1. Click the QuickBooks NEW / Plus (+) icon.
2. Select Bank Deposit.
3. Mark the invoice payment you received previously from the Select the payments included in this deposit section.
4. Expand the Add funds to this deposit section to add a new line item.
5. In the Received From column, select PayPal as the vendor who charged the fees. (I think this is the important bit)
6. In the Account column, add an expense account for the fee (I use bank charges)
7. In the Amount field, enter a negative fee amount.
8. Make sure the deposit matches the net bank deposit amount.
9. Click Save and close.

Now when you open the PayPal bank feed, it should show as an option to MATCH against the payment.