A ton of questions in there, so let's jump right in.
//I am currently pursuing Masters in Mech. Eng. in a top 20(in Mech) US university...Assuming that I maintain this GPA, would my Under-grad GPA still have an adverse effect on my chances of getting into the top 5 or 10 b-schools in the US?
Let's put this on the backburner for just a little while, tackle the other questions and come back.
//My understanding is that all the applicants are segregated into various applicant pools based on the demographic and professional field criteria. When I apply for an MBA, which applicant pool would I be put into?
Right now, I'd put you in the no experience category. Once you complete your Masters, get a job and spend a few years...that's when your real category will emerge. Anyway, these 'applicant pools' are subjective and not cast in stone.
//I mean to ask if I would be competing with an US applicant or an Indian applicant.
You are competing with every applicant who applies for a seat at business school.
//the big B-schools place a lot of emphasis on the company one worked for when evaluating the applications. Wouldn't I fare badly when I am compared with a domestic(US) applicant?
Not really. Big names help to an extent, but what's more important is your role, your accomplishments and your skills.
//do b-schools distinguish between applicants submitting GRE scores for GMAT scores.
Those that accept for GRE and GMAT scores don't differentiate between the two. They'd have some sort of a mapping table to compare the two, though. If not they'd end up comparing apples to oranges.
//Should I take one when I apply? Could you put the GMAT and GRE scores into perspective?
Take the GMAT anyway. It is accepted at more bschools than the GRE.
//And please share any other relevant points for people like me who have done their under-graduation in India and Masters in the US.
You have a slight advantage over the others who don't have any international educational experience. But the real differentiation will come from the work you do and the potential you can show to the Admissions Officer at the time of application.
So don't be too concerned about things [like the GPA that we now bring back from the backburner, now that we realise it's relative (in)significance] that you can't change.
Focus on making the future better than your past.