You will have to create two tax returns, one for you and one for your spouse when filing separately.
Using the desktop editions, after you have started the first tax return you can save the return at any time by clicking on the File menu at the top left of the desktop program screen. Then click on Save.
To start the second return, click on the File menu and click on New Tax return.
Note that filing separately is the worst way to file when married.
See this TurboTax support FAQ for filing jointly versus separately - https://ttlc.intuit.com/turbotax-support/en-us/help-article/taxation/better-married-couple-file-join...
