That would be a great addition to the current features that we have. I also hope to see this option very soon, @Hburke. 

We don't have an exact time frame on when the option to apply one payment to multiple customer accounts. Our developers might be working on making this function available for all. In the meantime, you can tune in for updates in our QuickBooks Blog.

For now, you can refer to the following article on how to record payments or partial payments for an invoice: Record invoice payments in QuickBooks Online. 

Your willingness to help Intuit improve our products and services is greatly appreciated. If you have other questions about invoices and or anything else, I'm happy to answer them for you. Just post it here as a reply and I'll take a look at it. Keep safe and have a great rest of the day!