You have a couple of options.
It is easier to prepare your tax return jointly for federal and separately for states using the downloaded version of the software.
Please see the link below for how to download the software based upon your reporting requirements.
Downloading TurboTax Desktop versions
You can also prepare your return using the online version of the software, but you will need to create a few files in order to file your state returns. Please see the following link for more details.
How to File MFJ for Federal but separately for state
Please see the attached link for more instructions on how to switch from filing jointly to separately. The link has the steps as well as other links that will be helpful to complete the process whether you prepare your returns online or using the download version.
Switching from Married Filing Jointly to Separately
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