Yes, your 12th percentage plays a great role here. To appear for Jee Main, you don't need to have any specific percentage, qualifying 12th standard, can make you eligible for Jee Main. But for admission to IITs that means to be eligible for Jee Advanced, one must have secured a minimum 75% marks (65% for SC/ST/PwD Category) or be in the top 20 percentile in class 12 or equivalent. Following 5 subjects will be considered for calculating the aggregate marks- Physics, Chemistry, Mathematics, Language( the one with highest marks ), any subject other than this four(the one wit highest marks).
http://engineering.careers360.com/articles/jee-advanced-eligibility-criteria