Replacement of marks of additional subjects and your main course subject is not like they will swap the marks you got in Hindi  and Mathematics on your marksheet. It works like if you calculate the total percentage you got in your class, you can take the marks of your additional subject to consider in place of the subject you have got the least marks in. CBSE schools consider this method only to release the merit list of their students.

If you're in 10th and aiming to get admission in 11th in any school, it depends on the schools if they consider your main five subject marks or the best five subject marks for the admission.

If you're in 12th and are trying for different colleges to get in, it depends on your course which you wish to study further and also some criterias and eligibility of the colleges. In most cases for general courses, colleges take the best three or best four subjects marks consideration for the admission process.

So, good luck.