It depends on the applying rules of the college. You have got to check the ordinances on the official website for that.As far as I know, a candidate applies under one category but if the rules are different for this, you must check it once.
If you think that you will not get a seat through MHCET test, apply by JEE score, if they have an option for that. Check last year cutoffs for both and talk with college officials. They will surely tell you which will be better in your case.
Good luck!