My first question about your situation is timing: If you apply to a f/t program this MBA season, you'd be starting in Fall 2010 - and it sounds like your MSc starts then too. So I don't know how you'd do both. Perhaps the school you're getting the MSc from has a good bschool and you can make it a joint degree? That would probably be the easiest route to pursue, in my opinion. If you apply in next year's bschool cycle, you may want to explain how it's worthwhile to postpone your career after X years of education (you wouldn't finish the MBA until 2013) and why you need all that as a foundation to the career path you have mapped out. As with any applicant, expressing how these educational programs (both the MSc and the MBA) are mandatory for your short-term goal is absolutely critical.
I've had clients with multiple degrees seem to have a tough time getting into bschool. While the top schools appreciate high academic achievers, I think they're also leery of people who seem to be collecting initials after their names. Bschool is essentially vocational training. The adcoms want to be sure you're going to take the education out into the world and apply it. So you'd need to emphasize to them how you're going to use the MBA and why it's a necessary addition to your other credentials. Your comment about applying the theory of the MSc could have some merit.
The only other question I have is that the most common pool of applicants who want to bring a Master's to bschool is the stereotypical Indian male engineer. If you're in that category, a pre-existing Master's won't really distinguish you; in fact, it may almost reinforce that you're in that class of candidate. This isn't a good nor a bad thing; you'll just need to differentiate yourself from that oversubscribed pool.
Hope this helps!
EDITED TO ADD: It does depend also on what the MSc is in. I assumed you were going for an engineering Master's but you actually didn't state that. If it's an MSc in Management, then many bschools could consider this comparable enough to an MBA program that the bar would be higher for you to explain why you need both -- and some top schools specifically preclude admitting people who already hold an MBA. You probably should contact the admissions offices of the bschools you're targeting to see what they say.
Lisa, Columbia MBA | Admissions Consultant | Elite GMAT Preparation and Admissions Consulting | http://www.VeritasPrep.com