As far as I know, when you create a new recurring invoice, you have a choice between “Off”, “Opt-In”, “Opt-Out”, and “Always” under the Auto Bill settings (top-right corner of the page). If you set that to “Off”, then it would not bill the client’s payment method (if one even exists), and would require you to manually enter a payment to close out the invoice.
That should allow the option to either have you enter the payment, or allow the client to manually use the online payment option (if you have it set up). I’m not 100% sure since I’ve never used it, but that’s how I understand it. I’m sure Hillel will be able to give a definitive answer.