Hey there, @aquinones.
Thanks for taking the time to reach out to the QuickBooks Community. How are you doing today? I hope all is well.
You can split your employees by filing your QuickBooks Payroll employees in QuickBooks and the others with a different program. Or you can file all your employees (including your QuickBooks employees) in a different program if you want to keep them all together. Either way will be just fine.
In the meantime, I'm including an article that covers how to file your employees W2s in case you may need it later on: File your W2 and W3 forms.
Please don't hesitate to let me know if there is anything else I can assist you with. Take care and have a great rest of your day!
