Hello CityHanfyman
To account for the credit card fees you can follow the instructions below on how to show this in QuickBooks Online:
1. Create the invoice for the full amount (fees included £100)
2. Receive payment to Undeposited funds (full amount)
3. Plus sign > Bank deposit
4. Tick the invoice on the top part
5. On the bottom where it says Add deposit, choose the same customer
6. Choose an expense account (say Fees)
7. Enter the amount as a minus figure (say -£2.98)
8. Now the deposit should be for £97.02 which is the amount they've received, and £2.98 should be on the fees account as the fee

9.If you have the bank account connected you will then see a match in for review
Any questions let us know
Emma