For automatic emails generated by the app (i.e.: outstanding invoice reminders, recurring invoices, etc.), you can set a generic email as the sender. To do that, first you need to create an Organization-Wide Email Address (go to Setup | Email Administration | Organization-Wide Addresses). Sample is shown below:
IMPORTANT: Ensure that the Organization-Wide Email Address is allowed for All Profiles.
After creating the organization-wide email address, go to Payment Center Settings and set the System-Wide Email Sender, as shown below:
The organization-wide email address defined earlier should be available in the drop down. If you don’t see the field (Sytem-Wide Email Sender field), edit your layout and expose the Visualforce Page SystemWideEmailSender: