Usually in the Indian Muslim format of castes, Syeds come in the GENERAL category when considered for any government examination or jobs. Along with Syeds, Sheikhs, Mughals and Pathans also come in the GENERAL category for not only in Joint Entrance Examination Main or JEE Main, but for all the government programmes or schemes.

So, you will fill the form according to the GENERAL category in JEE Main. Hope I have answered your question. All the best!