Since the S-Corp has to file it's own physically separate IRS Form 1120-S tax return and issue all owners a K-1 for each owner to use for completing their personal 1040 tax return, how you file your personal 1040 return is irrelevant and doesn't matter.
Though do keep in mind that for a married couple to file separate is nearly always the most costly way tax-wise for a married couple to file.
