Yes, you have to separately apply for IISER application form even though you are applying through JEE Advanced.

The registration dates has been released by the admission committee. The application form of IISER Admissions 2017 will be released on May 22, 2017

It is necessary to fill the Institution choice out of all 7 IISER for admission according to the preferences in the application.

To get admission in IISER you must qualify the JEE Advanced exam & secure a rank within 6000 in CRL.