Hello, and welcome to the Community, ourjoyfullife.
 

Multiple payments that have been taken can be applied to an open invoice, so yes you can apply different recurring transactions from a customer to one bill.

If you use QuickBooks Payments, Intuit handles everything after a customer pays for their invoice. Each payment will be processed and categorized into it's correct account. In the event that you're not using merchant services with us, there isn't a way to set these records up for automatic syncing with invoices.

I've included an extensive article which covers more information about recurring transactions and how they work: Using recurring transactions in QBO
 

I'll be here to help if you have any other questions. Enjoy the rest of your day!