CBSE doesn’t take best 5 or best 6 it will just display the marks of all your 6 subjects on marksheet . Now it depends on University to university and course to course, that they take best 4 or best 5 .
6th subject has additional profit when you are failed in one subject then your additional subject will replace it.
For example in Delhi University for BSC computer science (Hons) the admission would be based on the aggregate of marks scored in class XII in best four academic subjects inclusive of one language, Mathematics and two out of Physics, Chemistry and Computer Science/ Informatics Practices.