If you would like to collect a payment on your customer's account for a manual invoice you can take the following steps.
First, you will want to ensure that the online payment option is enabled. To confirm this, in your Recurly site navigate to Configuration then, Hosted Page Settings on the left-hand side and enable Account Management Pages. Then, you will also want to check the option to Pay Invoices Online. Once the online payment option is enabled navigate to the invoice within your customer's account and go to the Invoice Actions dropdown menu at the top right-hand side and View Hosted Invoices. This will take you to the invoice specific hosted page where you can either use a card on file to pay for the invoice or provide updated billing information to pay for the invoice. You can also provide your customer with the invoice specific link where they will be able to make the payment as well. This process is required because manual invoices are intended to record payments that are received outside of Recurly but this option will permit your customers to pay via the billing information that is provided.
Additionally, once you've enabled the Pay Invoices Online option via the Hosted Page Settings you do not need to enable it each time a manual invoice needs to be paid. This will now be a global settings available for all manual invoices.