You can file Married Filing Separately or Married Filing Jointly whether your spouse lives with you or not. To file Head of Household you must have dependents that live with you for over 50% of year and you pay over 50% of their expenses. So if your son lived with you less than six months of the year (or otherwise supported himself) you can't take the deduction for him. He should file his own return if eligible. If he's not required to file a return I think you could still list him and just not take the deduction.
