Hii phani,

To get a seat in M Tech through GATE,you need to have a graduation degree.

By the time you complete your btech you need to complete all your arrears.It doesn't matter about the arrears when you take the exam.If you can complete all the arrears by thr time of counselling.you can get the admission in IIT irrespective of your GATE score.

If you are not able to complete those arrears by the time of counselling you won't get an admission in IIT.

So complete all your arrears as soon as possible.

All the Best...,