Yes you enter all her info, income and deductions.  On most things it will first ask who the W2 or 1099, etc belongs to.  On a Joint return when Turbo Tax says YOU is usually means either of you.

When you enter your name at the beginning under Personal Info you pick Married and filing together then it will ask for the spouses name and info.

FYI sometimes people don't know a Joint return is 1 return for the both of you combined.