There could be one problem is of being eligible for that college because some of the colleges make it as an eligibility criterion to have more than 50% in 10th, 12th and graduation. So you won't be eligible for those colleges. But many of the colleges keep eligibility criteria as 50%+ only for graduation. So there you have a good score and you can definitely apply for it.

After you give MBA exams like CAT, XAT, CMAT, MAT, SNAP, NMAT etc, then all the colleges in which you apply for admission  makes a merit list to call students for second round of interview and WSAT which is made in the basis of your aggregate score and which is based on different parameters such as MAT marks, 10th, 12th and graduation percentage, work experience, engineer or non-engineer, gender, extracurriculars etc. whose weightage vary according to different colleges.

In this weightage of academic records is generally approx 10-25%. In which 12th class weightage varies from 5-10%. In this first merit list, most of the colleges give highest weightage. So to cover a little loss due to 12th exam percentage you can score very well on MAT exam and you can get calls from most of the colleges.

So, make sure you perform well and select colleges accordingly you will have a good chance to end up in a good b-school.

All the best!!