For an existing invoice I have agreed a lower payment to settle. How do I do this on QBs so account shows as cleared?
You can either change the amount of the original invoice, or create a credit note for the amount you have reduced it by, apply this against the payment so that the open balance remaining is what the customer actually paid you. It's up to you how you would like to record it.
Let us know if you need any further help with this,