https://engineering.careers360.com/articles/jee-main-eligibility-criteria

The above link will show you what is the eligibility criteria for JEE main. According to this, you need at least 50 in each subject, while your aggregate in PCM(physics, chemistry, and mathematics) should be not less than 75%. Your eligibility percentage for JEE main will be calculated by PCM subjects only.

As far as Boards are considered, 5 subjects are considered in CBSE including English as it is mandatory. But as you mentioned you have more than 5 subjects in your class 12th, so the best of 5 subjects will be considered i.e. top 5 subjects in which you have the highest score.

In ISC also English is compulsory for calculation of board marks, apart from that 3 subjects are considered in which you have the highest marks.

in case of admission to certain universities such as DU, where your Board marks are considered, marks of Subjects such as Physical Education don't matter. They just want your PCM/B marks and English.

Hope this helps

Regards