In this case I would say you should provide the percentage on the basis of all the 6 subjects. See in the official website there are no mentions about this so its safe for you to consider all the subject rather than considering the best of 5.
To know more about MHTCET visit the link below:
https://engineering.careers360.com/articles/mht-cet
I hope this answer helps. All the very best for your future endeavors!
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