Yes there is separate registration.

KEA will conduct the counselling of BAMS & other Ayush programme for the Government colleges. The link to admissions to the AYUSH courses through CET is expected to be made available under the CET section on the KEA homepage given below

http://kea.kar.nic.in/cet_2018.htm

The candidates who have completes their document verification by 27th June can visit KEA website to keep track of when the notification about the AYUSH counselling is released.

In order to get admission in private Ayush colleges you need to apply indivisually to the particular college in which you want to apply.

Good Luck!