I've just sent my last invoice for potentially 2/3 months is there anything I can do with the monthly payment for this service?

Hello there, threadgold_10.

If we've created one invoice for multiple items of your customer, we can record a separate payment for each of the items. We only have to make sure that the dates are correctly set. It'll automatically deduct the customer balance every time we record a payment.

To guide you further with this, you can check a few ways in recording the payment in QuickBooks Online. Visit these articles:

• Record invoice payments. 
• Record a customer refund.

Please know that I am always to help you in case you need one. Thanks!