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Very well done overview of Intuit Payroll features
Using Intuit to make employee check stubs is actually very simple. Check stubs for employees will be printed as part of a normal payroll run. Note that you can print payroll locally, in which case you'll also print the stubs, or handle it electronically, in which case the stubs will be distributed by Intuit.
If you decide for electronic payment, the money will transfer to your employee's account without your having to write or print a check or stub. They'll get the stub as part of that process in the mail. So you don't have to worry about it.
If by that you mean downloading the information to print paychecks, yes. Using Intuit Payroll/Quickbooks will allow you download/create anything you would like about paychecks.
The Intuit Online Payroll system is an add-on to the Quickbooks online product. Since payroll is integrated so closely with the other parts of business accounting, it makes sense to do your payroll with the same company and software you use to do the rest of your accounting.
If you use the Intuit payroll product, you can reach them on the phone at 800-624-2106. Also, there's a web page that you're encouraged to use -- it may answer your question faster than making a long call. http://payroll.intuit.com/support/contact/