It's generally best for married couples to file as Married Filing Jointly. There are several credits that are disallowed when your filing status is Married Filing Separately. See this resource for more information:
https://ttlc.intuit.com/turbotax-support/en-us/help-article/taxation/better-married-couple-file-join...
With either the Married Filing Jointly or Married Filing Separately filing status, you will receive a Schedule K-1 from your S-corporation tax return. This is how the income from the S-corp will flow through to your personal tax return.
I would definitely recommend filing together to make sure you have every opportunity to get all tax credits that are available.
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