I want to setup several recurring invoices for customers that pay by direct debit. My old s/w allowed me to add a payment to the invoice in anticipation of it been paid.

I can share some information  @info-badgeralarm. 

Currently there is not a recurring payment option so that you could pre mark the recurring invoices you create as paid. You can create a recurring deposit or recurring journal entry separately for payment however you would still need then to attach the recurring payment to the invoice itself.

You can connect the bank account in Quickbooks which will work to match the payment received with the invoice or you can manually create the payment on the invoice

Also you can let your QuickBooks Online (QBO) account know that those invoices we’re paid already by processing a receive payment. This is the only way to mark an invoice as paid in QBO.

Here’s how to record a payment:

1. Go to the + New button and choose Receive Payment.
2. Set the Customer, Payment method, and the account you put the payment into from the Payment method dropdown.
3. In the Outstanding Transactions section, select the checkbox for the invoice your recording payment for.
4. Click on Save and close once you’re done. 

Once you’re done, you can run a Customer Balance Details report to check the remaining balance for your customers.

You can refer to this article for more information about receiving payments and the report that I'm referring to above: Record invoice payments in QuickBooks Online.

If you have multiple payments recorded as a single payment, you can check the following guide on how to add them to your QBO account: Deposit payments into the Undeposited Funds account in QuickBooks Online.

I'm always here if you have follow-up questions in recording invoice payments and or anything else by leaving a reply below. Take care and have a great rest of the day!