Manual payments in this context refers to the Test gateway. There is an addon for supporting subscriptions in gateways that do not support automatic renewals slated for release soon.
There is no way to disable the parent invoice. You do not have to worry about generating two invoices since your customers already expect to receive an extra invoice whenever a renewal payment is processed.
What is in the error email that WordPress sends you? In addition, kindly attach a sample “view invoice” link (the one you receive in your invoicing emails) in a private reply.