After reviewing further, your best bet is going to be to create a MFJ return for Federal purposes and utilize the check boxes available in Screen 1, Filing Status.  Here you can check "MFJ vs MFS Comparison" and "Live With Spouse?" if applicable. 

This will create a MFJ/MFS Wksht where you can verify the amounts going to each person when split to MFS.  Any adjustments should be made using the T or S indicators within each field (or TP SP columns in certain input screens).

Once complete you can click the "Click here to split this return" located at the top of the worksheet. This will result in 3 files: 1= MFJ Federal 2= MFS Taxpayer 3= MFS Spouse.  

Select the applicable split spouse to add CT to for the purpose of filing the state.

For more details see: https://proconnect.intuit.com/support/en-us/help-article/tax-filing-status/generate-mfj-vs-mfs-compa...