Sorry for your loss. You would file two separate returns. If you are using the Online version, you need to create two separate accounts (UserID and password), one for you and one for your mother's.
The better choice for more than one return is the Desktop software. If you are using the Desktop software then once you finish one return, close & save it, then click on the File menu and choose New Return.
When you do your mother's return, start the TurboTax interview, under the Personal Information section, you should choose "I'm preparing this return for ______ who is deceased". Next, you should enter the date of death. From here you can prepare his return as you normally would.