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The percentage criteria by CBSE is "the marks of that additional subject are considered in which one scores higher". The CBSE board has a best of five rule in which your main percentage is decided by one language subject I. e. English and other 4 subjects in which you get high scores. And the remaining subjects becomes additional whose marks won't be added to your main percentage. The subject you would score the lowest will automatically excluded. So, if you score higher marks in Physical Education than any of your subject other than English then it would automatically replace the lowest scoring subject. So, your percentage should calculated by adding marks of English (Mandatory), Physics, Chemistry, Biology and Physical Education. As you said you socred the lowest in maths it would be replaced by Physical Education.

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ATMA Eligibility Criteria 2020
Candidates must adhere to the eligibility criteria of ATMA 2020 before filling the application form. The ATMA eligibility criteria 2020 prescribes the educational qualifications and age limit required by the students. Candidate must be a citizen of India to be eligible to apply for the ATMA 2020 May session. Students must possess a Bachelors's degree or equivalent qualification from a recognized or statutory university. Students must obtain a minimum of 50% marks in aggregate in the qualifying examination. Whereas, aspirants belonging to the reserved category must obtain a minimum of 45% marks in aggregate. Candidates appearing in the final year of the qualifying examination can also apply for ATMA 2020 May session. ATMA 2020 eligibility criteria do not prescribe any upper age limit and requirement of work experience to appear for the examination.