on the separate return make sure married filing separate is the filing status. you can use single and there are certain tests you must pass to use Head of Household.
with the lower income your taxes will drop a lot but when he goes to file his return his taxes will likely increase a lot. probably more than your decrease. also both of you must use the same method for deductions either standard or itemized. in addition, if you are both qualified to claim any children, the rules state that only he can because he would apparently have the highest AGI
what amount is showing up as code w on your w-2
checking family for the entire year is correct since that's what you had.
if you are doing a married filing separate return, you must use form 8889-T not the S.
you cannot use a joint return to do married filing separately.
you would need to create a new account and start a MFS return.