We answer many questions here, and usually it is straightforward enough to show a user the advantages/disadvantages of MFS vs. MFJ. Personally, I do not think you should be seeking advice here from us. Your situation is too tough for us. You have an incarcerated spouse who clearly has been dishonest in the past. So if you ask how she filed, will you rely on the answer? Please seek help with this from your attorney to find out how she filed or even if she filed.
You could buy some time by getting an extension--an extension does not give you extra time to pay but it would give you extra time to sort this out and file your return.
https://ttlc.intuit.com/community/extensions/help/how-do-i-file-an-irs-extension-form-4868-in-turbot...
If you are getting a refund, there is not a penalty for filing past the deadline. If you owe taxes, the interest/penalties will be calculated by the IRS based on how much you owe and when they receive your return and payment. The IRS will bill you for this; it will not be calculated by TurboTax.
Edit a few minutes after original reply----Another reason to wait to file until you sort this out is that if you make the wrong choice--after the filing deadline on July 15, 2020, you can amend a Married Filing Separately return to change it to married filing jointly, but after the deadline you cannot change from joint to separate. So if you file a joint return and want to change it--it will be too late.
**Disclaimer: Every effort has been made to offer the most correct information possible. The poster disclaims any legal responsibility for the accuracy of the information that is contained in this post.**
