Yes its a separate process. Government has reserved 85% seats for the students of its own state and 15% for ALL INDIA QUOTA in which students from all over can apply. Generally the cutoffs are different for the AIQ and state quots. AIQ cutoffs are comparatively higher so you will face a heavy competition.

Refer to the website below for more detailed information...

https://news.careers360.com/neet-2020-nta-releases-notice-for-15-aiq-state-of-eligibility

Best wishes. Thank you.