R12 Payments of employee suppliers for both positive and negative payments

Attempting to upgrade from 11i to R12, need to pay suppliers who are employees separately from those suppliers not employee.  Thinking about setting up a Payment Method wth a new rule where Payment Process Type is EQUAL to Exployee Expense.  Here the wrinkle in this plan, we will have both negative and positive payments for these employee suppliers.  Can a eText RTF template be used to produce two output files (one for positive payment and other negative payments).   The negative payments would go to our external payroll application for deduction from employee paycheck, while positive payment would go to bank as EFT payments.  Is this possible or does