Do I need to apply to PGDM course even though I will through CAP round through CET? Is there any different eligibily for intentional place?

When you get admission through CAP rounds, You are by default applying for MMS course. For PGDM course, you need apply differently through online forms that are available.

The PGDM course is a separate course by Wellingkar which is not under the Mumbai university thus a separate application is required and selection is not as per CAP allotment. The MMS course which is under Mumbai university requires only the CET CAP allotment process.