Not file separately but you need to enter both of them into your tax return. Did you already file a tax return? After you enter the first W2 you can add another W2. If you already filed your return you will have to file an amended return to add another W2.
To add a W2 go to
Federal Taxes Tab
Wages & Income
Wages and Salaries- Click the Start or Update button
Then if you are married you should have 2 buttons...Add w-2 for (taxpayer name) and Add w-2 for (spouse name). Click on the correct button to add a W-2.
This answer has been verified for accuracy by an Intuit expert employee
