How to make up for previous unwithheld payroll payments?

by JC
(Texas)

We are a small church that is planting. I am in the process of setting up payroll for our 2 employees (pastor and music director). I have made 2 payments for them but they were lump sums. Therefore, they did not have anything withheld from their paychecks.

As I am in the process of setting up payroll via Intuit, I was asked if the church/business will pay for the make-up withholdings or if the employees will make it up by withholding more from their future paychecks between now and the end of the year.

Does anyone have advice on which option I should go with? Or has anyone run into a similar circumstance?

Thanks in advance!