You should enter the total marks for all 6 subjects, including Physical Education.

Some colleges use the best 5 subjects to admit you in their institution; however, do not write something wrong in your application form.

This is why:

Consistency: You will be consistent in all academic records by using the total marks for all 6 subjects.

Eligibility Criteria: Certain colleges/Institutes will have merit-based eligibility criteria on the basis of total percentage of marks scored in all subjects.

Verification : You can be asked to present the mark sheet containing marks of each subject at the time of verification.

For improvement exam:

In case improved marks are greater than the original marks, you can alter your application of JEE Main using the new marks.

Generally, there is an opportunity through the NTA for applicants to effect corrections or updates on their applications.

Retain copies of the original mark sheet and the enhanced mark sheet

Ensure you provide accurate information and follow all the rules and guidelines given by the NTA to avoid possible mishaps in the process of making an application and counseling. https://engineering.careers360.com/articles/jee-main-counselling