Hi Jatin,
IT221 is used to enter anything that was entered or paid outside SAP system for record keeping and reporting through SAP. It would not pay any amounts to employee.
If you would want to enter the manual check number under the field Check number in IT221 that should be fine as it waould say the manual check was paid and just neing entered into the system.
You need to make sure about the tax reporting for the amounts being paid or deducted while running an IT221 adjustment.
Thanks,
Ameet