Are you using Home & Business on Windows or Mac? On Mac you can only use the Quick Employer Forms. In Windows you can do them 2 ways.
You can do separate businesses. Do one then start over to do another company.
In the Window's Home & Business or Business Desktop program to Prepare W2s or 1099s, go to Start a New Return or File-New Return.
Then on the next screen it asks What would you like to do?
Check the circle that says Prepare W-2s and 1099s for my employees or contractors. Then that will expand and give you a choice to prepare them online or on your computer.
If you select to do them online using the Quick Employer Forms the forms are efiled to the IRS. You then print the copies to give out to your people and print copies for yourself. See this for more info…..
https://ttlc.intuit.com/community/forms/help/what-is-quick-employer-forms/00/25916
If you select to do them on your computer you are responsible to mail the forms to the IRS.