Hello Paula,
Welcome to the community and thank you for posting your question.
You can use the following process to record what we call recording Bank Charges but in this case its Fuel costs not bank charges.
You should already have an invoice created.
Mark this as paid in full but make sure it is deposited to un-deposited funds.
Once you have done this, Save and close and then you need to create your bank deposit.
Click on the Plus icon and then choose bank deposit.
At the bottom of the deposit once you have selected the funds you need to transfer from un-deposited to your bank account you need to create a line that reflects what has been deducted.
So you could use a fuel account make sure you use the customer as the "Received from" in the amount box you will then put a minus figure to show the funds were not received but actually deducted from the Deposited balance.
You can then save this transaction and this will then be correctly recorded so that the transaction will then match with the bank feed but also not leave an open balance on the customer's account.
Hope this helps and if you need anything else please do let us know.
Thank you.