You can still file as Married Filing Joint even if you are living separately (& even if only one spouse has income), you both must agree to file Jointly. You enter the address on your tax return that you would want the IRS or State to contact you if they needed to. The program will also ask if either of you lived in a different state. You both would have to file separate State returns, depending on your State's filing requirements.
Also, when married & living apart you can also file as Married Filing Separate (each file their own tax return & enter their own information), or Head of Household, if you quality.
