In the Admin: Users: User Profile: Payment Methods page, there is an Actions menu to the right of the row showing the bidders credit card details. The action menu has a drop down option called, 'Collect Registration Fee'. This will allow the admin to enter any amount to be charged to the bidder instantly.
There is a corresponding Email Template called, 'Bidder: Registration Fee Received' that is triggered and emailed to the Bidder whenever the admin charges a bidder using this feature.
Note: This subject & body of this email template can be customized.
Note: The admin can disable or deactivate this email template and bidders will NOT receive an automated email when the admin charges a bidders credit card using the above process.