Get your taxes done using TurboTax

Yes you file all both income on the same tax return.  You enter your spouse's income the same way as yours.  When you start entering a W2 or 1099 it will ask who it belongs to.  Like for W2, after you enter one you add another.  Click on Add for "John" or Add for "Mary" at the bottom.  

Did you enter their name under My Info or Personal info when you entered your name and picked Married filing together?