Do I have to say that I am married even though legally I am

[KarenL2]

Yes.  If you are married you do have to state on your tax return that you are Married.

[californiasteven]

If you and your spouse were not together and you were taking care of a child TurboTax will suggest you file as Head of Household.  But you do report that you were married.

[KarenL2]

Yes.  When you enter your spouse's information, there should be a series of questions to answer.   One question will ask if you lived together during the last 6 months of the year (July 1st - Dec 31st).  If you did not live together (at all) during that time, the software will allow Head of Household.