Hello dmbirdplumbing,
Welcome to the Community - thank you for your question!
You can either edit the original invoice so that the amount due is the amount you received, or you could raise a credit note for the amount left and apply this to the payment to close it down.
You can do this by going to the + icon, selecting credit note and selecting the customer. Once you have created the credit note, open the payment and tick the credit note at the bottom.
Thanks,
Talia