Why have you decided to file as Married Filing Separately? That is the worst way to file a tax return when you are married.
See this TurboTax support FAQ for filing jointly versus separately - https://ttlc.intuit.com/turbotax-support/en-us/help-article/taxation/better-married-couple-file-join...
The payment made with the extension can be either divided between you on separate returns or you can have the payment on one return only.
