Apparently this wasn't thought out to far. I have the same issue. I can create the invoice in Base and the pipeline to create the invoice in Books works flawlessly - but how am I supposed to apply payments?
I've got an open support case with Base and they've simply stated, "I will reach out to the Pipelines team to see if there is a way to interact with the Payments aspect of an invoice within Quickbooks. Once I have more information I will let you know!"
Seems odd to me; like paying $20 for a $16 item and not getting any change back. They go hand-in-hand.