1.You can't, you must have 2 accounts. One for MFS and one for MFJ.
2. You need to prepare CT, not file, to determine the tax liability and amount allowed as a credit for NY.
My thoughts and maybe helpful advice:
If it were me, I would see how much the CT tax is for joint before doing more. You can file MFJ for CT as nonresident and claim just the CT wages. CT prorates tax based on your full income for the year so you would pay a little more in CT tax to file jointly. Sometimes the hassle of an extra mock federal return is not worth the trouble and sometimes it is.
If you don't like the tax bill for married filing joint in CT, you need to create a second federal return of MFS and use that to create you CT return. Realize, paying for an extra filing may be more expensive than the tax difference. Take a look at the numbers and trouble and decide what works best for you.
Once you decide which CT return you want to file, you can finish your state return with the correct tax liability for a credit. If you are doing CT as MFS, you don't want to do it in your MFJ return, just add the credit against NY.
If you are using the online program, you have to create another profile and create the new MFS for fed and CT. If you are using the desktop version, you can add another return.
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