I am filing for my late mother. When asked, does the word "you" refer to myself or my late mother?

TurboTax is sorry for your loss.

If you are filling the tax return for your late mother, then the word "You" is referred to her.

To make sure whose tax return file it is, please go to the menu on the top left of your screen. Check under "Balance Due" to see the owner of the tax return. 

Thank you for using TurboTax.