I found KB48078 article on "How to process a manual payroll check".  The steps seem exactly the same as a normal payroll run. I do recall reading elsewhere that you can enter in a check number for an employee if a handwritten paycheck was issued to an employee.

To avoid hand writing checks, we used to "advance" employees their final pay when terminated with an Accounts Payable check, using the A/P QUICK PRINT feature.  Then, when the next Payroll period ended, we would enter the hours and other information... and deduct the advance which would cause the net payroll check to be $0.00.  However, this would cause the employee's YTD earnings to be correct, which is what we want.

I may be making a mountain out of a mole hill, but here are the questions of my confusion:

1.  Can you have multiple payroll check runs with the same Period End Date?  In other words, if we run a complete payroll run each time we terminate an employee and want to issue a final check using our "normal" Period Start and Period End Date, will that cause any problems when we use the same Period Start Date and Period End Date for the remaining employees when the next, upcoming, "full" payroll run occurs?

2.  Three dates are required when running a payroll.  Period Start Date, Period End Date, and Check Date.  Can the Check Date be before the Period End Date?  For example, if the normal payroll period is 10/08/2018 - 10/21/2018 and the normal check date is 10/29/2018.  But, an employee is terminated on 10/14/2018 and the state requires that they  be paid within 48 hours. Can we run a payroll just for that 1 employee using start date of 10/08/2018, end date of 10/21/2018, BUT check date of 10/15/2018?  I would hate to jinx our big payroll run by testing a "terminated employee payroll run".

Thanks!