We accept Amex. If we take £100.00 they only pay £98.10 less the 1.9% charge. Our bank account is linked to QB. How do I reconcile the difference?

I'll guide you through recording bank charges from your customer payments and reconciling your bank, @oakleighphysio.

We can receive a payment from the transaction created in QuickBooks Online (QBO). From there, we can put the transaction in the Undeposited Funds. Each bank deposit creates a separate record in QuickBooks. Make deposits one at a time for each of your deposit slips.

Here's how: 

1. Select + New.
2. Select Bank deposit.
3. From the Account ▼ dropdown, select the account into which you want to put the money.
4. Select the checkbox for each transaction you want to combine.
5. Make sure the total of the selected transactions matches your deposit slip. Use your deposit slip as a reference.
6. Select Save and new or Save and close.

Additionally, you might want to check this article and learn how to track your cash flow in QuickBooks Online: Use reports to track cash flow in QuickBooks Online.

It's always my pleasure to be of assistance. I'll be here if you've got additional queries regarding bank reconciliation in QBO. Have a good one.