Will lesser percentage in 10th and 12th standard anyhow effect your selection in good IIM's inspite of having good marks in CAT examination?

Yes it will be a problem as most of the IIMs Devote 10-30% in the final selection score for academics and others use them while rolling out the interview calls.

However it does not mean that it is difficult to get through because they also consider CAT score, work experience, diversity and WAT Personal Interview scores during selection with interview having the highest weightage.

Hence score a high percentile and add to your chances of final selection

All the best