If you lock the employee record in IT0003, the employee won't be considered during the "regular run".
I would suggest that you let payroll be calculated for that employee (or do a Payroll Simulation), create an IT0015 with a Deduction equivalent to the Net Payment, and then re-calculate the employee's pay (which should now show Zero Net Pay). If you have one, use the "Miscelaneous Deduction" WT (the one that is not linked to a Third Party).
When you will be "paying it in Full & Final Settlement", you then create an other IT0015 with the same Deduction WT but with the Amount in negative.
