No marks of CS will not help in IIM.The two are different from each other.For MBA you need to possess graduation degree from recognized university and CAT percentile.

You will have to be a graduate and CS alone will not help.
Aim above 50% minimum to be eligible to apply for CAT entrance and other management entrance.
Your academic records are definitely helpful but there are many other colleges which are not strict at past academic records.
You should also aim at applying in other exams apart from CAT like XAT (application has started). CMAT, NMAT, MAT etc..

In IIM's your past academic does matter and you will also have to aim above 99.5 percentile to get into top ones.
You can check eligibility and selection process for top 3 below:
IIM A Selection Process

IIM B Selection Process

IIM C Selection Process

Hope this helps.