Hello Faizan!
Excellent question! In short, Konrad is correct. An exam that counts towards multiple certifications need only be taken one time. The only time you need to be concerned is when a single exam can satisfy a couple different areas for the same certification.
In that case, the exam will only count towards the one area, and you will have to pick an alternate exam to satisfy the other requirement.
In my own case, I had taken 70-620 as part of my MCSE 2003. and when going through the upgrade path to achieve my MCITP: Enterprise Administrator, I did not have to satisfy that requirement, as it was already taken for the prior certification.
As it turns out, I am actually an MCT (Microsoft Certified Trainer), and would be glad to answer any and all questions that you may have about the upgrade process. TechMyWay Training. where I train, actually offers a pretty straightforward upgrade approach
for the Enterprise Administrator cert here:
http://www.techmyway.com/Courses/Certification.aspx?course=7.
If you would prefer to upgrade to the Server Administrator cert instead, check out the required exams here:
http://www.techmyway.com/Courses/Certification.aspx?course=8.
Good luck in your endeavors moving forward, and if I can help you at all to that end, just let me know!
Very Respectfully,
Josh Blalock, MCT
