There is one of 2 solutions that will work here.

1. Default the online payment off so i can add charge for CC payment. Regardless of previous transaction. make a option. Then you send invoice as normal. If they want CC payment then i can add the charge and give them access.

2. Add a request to pay by CC button and when clicked add a convenience fee tot eh invoice and enable the online portal. This way when they click the link it runs the macro to do this. On in zoho world it is a function)