Follow these steps since NJ allows separate filing:

1.  File the federal return
2. Use the Split MFJ Return Tool:  
   1. Go to the File menu and select Split MFJ Return.
      • ProSeries will create two new, separate client files (one for the Taxpayer, one for the Spouse).
      • Note: If you are in ProSeries Basic, you'll have to do a Save As and manually delete the other spouse's data.
3. Prepare the "State-Only" File:
   1. Open the new MFS file for the NJ resident spouse.
   2. On the Federal Information Worksheet, ensure the filing status is Married Filing Separately.
   3. Crucial Step: In the Electronic Filing section (Part VI), uncheck the box for Federal e-file and check the box for New Jersey e-file. This allows you to transmit the NJ return as a "State-Only" (unlinked) return.
4. Attach the Explanation:
   1. Since you are filing MFS after an MFJ federal return, NJ often looks for the "Special Circumstance."
   2. In the NJ resident return, look for the NJ-1040 "Notes" or "E-file Attachments" section. You can often attach a PDF labeled "GIT-4 Disclosure" or "Filing Status Explanation" to the electronic transmission to prevent a kickback or manual review letter later.