Payment Groups containing multiple Payment Methods: How do we create a Payment Process Request when

The client here wants to process payments across operating units and entities, by Payment Groups.  A payment method of Check may have multiple Bank Accounts, As is the case for most of their payment methods.  If we create a PPP and select Payment Groups and a payment method of "Check", how can we a) select the correct bank account or bank accounts?  How can we ONLY get from the Multiple Payment Groups ONLY those invoices that are associated to customers with a Payment method of "Check"? 

Next Question:  If we can't do as the client requests and schedule payments by Pay groups containing multiple payment methods, What would be the next best option?  Multiple Templates?