Recurring Payments can be created on their own, not applying to an Invoice, or to All Open Invoices or a Single Invoice:
Based on your Interval the system will show you when this will process
Then whatever amount you set will be processed on that interval and then be applied to the oldest open invoice first, then roll over into the next one until all invoices are paid. If new invoices get added they will just but added at the bottom of the next invoice to process against, by Invoice Date.