You need to attach this information to a pay run. If the payment is a one-off such as a bonus or termination pay, you will want to create an off-scheduled run. Off-schedule (or Ad-Hoc) runs allow you to add only the employee's and payroll instructions you need. If the payment is a regular pay for the whole pay period, you will want to create a regularly scheduled run. Regular pay runs include all employees and all expected payments for the pay period.
Once you have a pay run created, and you have entered the input sheet, you are ready to record the manual cheque payment.