Your query is not clear for me.
In SAP, the IT0007 will define if the employee will be paid automatically (Negative Time) or if Time entries will be required for the employee to be paid.
With that in mind, your "Contractual Employees" could be considered Regular Employees or Casual Employees, depending on wether Time Entries are required for them to be paid or not.
If all your employees share the same Payroll Period and Payroll Dates, you should be able to achieve your requirement with a single Payroll Accounting Area. Variations in Employee Groups and Sub-Groups should enable you to get the result you require.