Please clarify the examination or institute for which you are seeking information. There are many institutes and many exams and admission process of all are different.
If you are looking for All Indian Quota Seats in Medical Institutions based on AIPMT Examination, you need not to applying anywhere. Simply appear for the examination and attend the counselling.
To know which all institutes participate in AIPMT Counselling, refer to its Information Brochure.
Many other institutes also take admission based in AIPMT rank but conduct their own counselling. For such institutes (like AFMC) you need to fill separate application form.
For other institutes like AIIMS, JIPMER, CMC & Others you need to appear for their own entrance examination.