If you're setup for auto-payroll, there isn't a need to write a paper check since QuickBooks payroll service will automatically create the payroll check for you, whether it's a manual check or direct deposit.
All you have to do is to print the manual check created and send it over to your employee. To create a paycheck manually, here's what you'll need to do:
In left menu, click Workersor Payroll.
Go to the Employeestab.
Click on the green Run Payrollbutton.
Choose the worker you'd like to pay, then enter their hours.