Hello Sayali

Yes, you need to separately apply for Ayush Counseling and Maharashtra state counseling. The following are the websites for the same :

http://aaccc.gov.in for AYUSH

https://www.google.com/url?sa=t&source=web&rct=j&url=https://info.mahacet.org/CAP2021/NEET_UG/&ved=2ahUKEwiR2ISPn8z0AhXNfd4KHZvQAocQFnoECBAQAQ&usg=AOvVaw3sqVCwK7taH_XzYnHRe49c for Maharashtra state counseling. Hope that helped. All the best.