If unluckily I would get less than 60% in 12 boards but I have already got EEE branch in KIIT during KIIT Counselling, then will I get admission there?

In case you have secured less than 60% in the higher secondary examination, then it is best to sit for the Improvement examination. 

If you even secure admission at KIIT or any other relevant institute for a course, it will ultimately go in vain if you become ineligible to sit for any company exam. Around 90% of the on-campus companies arrive with a specific cut-off where the minimum criteria set is 60% in 10+2. 

So, taking an improvement examination is the better option.