Hi Soman

The admission into Sir J.J College of Architecture is primarily based on the NATA scores only, but on their official website, they have also mentioned about the JEE score card. so I think they admit students based on both NATA and JEE Mains Paper 2 scores. For the details regarding admission and the enclosures refer:
http://www.sirjjarchitecture.org/admissions.html
On this website, you will get a PDF document which gives you the details of B.Arch admission through both NATA and JEE Mains Paper 2.