Hello aspirant
Actually the best of two in JEE Main is taken on the basis of total percentile.
Subject wise best of two percentiles is not considered
For example, you have overall percentile 96.40 in January with 98.50 percentile in maths and in April you have total 97.60 percentile with 96.00 percentile in maths, then your final percentile will be considered of April as it is the best of two. Although your maths percentile is better in January, it is not considered as in JEE main, only total percentile is considered whatever the subject wise percentile may be.
Hope it helps!!