Anusha,
Why can you create each employee as vendor and post invoice for payroll related data, and then try to execute the APP (F110) for each vendor, then use the FCHR (online cashed Checks) for check encashment and clear the subaccount and update the balance in main bank.
Invoice:
Payroll expenses Dr
Employee Vendor Cr
F110:
Vendor Dr
Payroll check clearing account Cr
FCHR:
Payroll check clearing account Dr
Main bank A/C Cr
Note: The above process will applicable only if you are paying through checks.
Regards,
Ravi