Hello there, usercheryle.

Splitting employees between two different programs in QuickBooks can be done by assigning each employee per class. I'll show you how:

1. Log in to your QBO account.
2. Go to the Gear icon.
3. Select Payroll settings.
4. In the Accounting section, click Edit.
5. In the Accounting Preferences window, scroll down and click Edit under Class Tracking.
6. Choose I use different classes for different employees.
   
7. Choose a class per employee.
8. Hit Save.
   
    

Then, run a payroll. We can use this reference for further guidance: Create and run your payroll.

On the other hand, if you want to run a payroll with a different class each time, we can send this feedback to our Product Development Team. Gear icon> Feedback.

We can visit these articles for additional information when filing your W-2 form and generating reports:

• Learn when and how to submit your W-2 forms to Federal and state agencies.
• Run payroll reports in QuickBooks Online Payroll.

Let me know if you have more concerns about running payroll in QuickBooks. I'll help you in any way that I can. Take care.