The best of CET and JEE marks will be considered for admission in the all India Quota seats.Suppose you have applied 10 colleges and according to your preference if you are getting clg no 7 by cet and clg no 6 by jee then clg no 6 will be alloted to you.You can check the college cutoffs for 2013 as that year also considered both cet and jee(2014,2015 didn't had cet and 2016 gave preference to cet marks over jee) like now to get a fair idea about cutoffs. Do remember that at that time jee mains qualifying was 114 so 114 of 2013 = 81 of 2017.

Refer this article to get clarity on whether mhcet marks or jee marks will be used for admission in All India Quota.

CET not mandatory next year for all-India quota admissions - Times of India