If the a/c is 747 All Series Passenger it will be the old configuration. So no lie-flat seats in C.

I agree with going for the upper deck but be aware of the small overhead compartments. If you are carrying a standard sized piece of hand luggage you might have to store it downstairs.

On my last flight on this type of a/c I sat downstairs and it was not that bad. The isle between the rows is huge and it was nice and quiet through out the flight. But then on the other hand: I only paid a PE fare from CPH and not a C fare from MAD.

As most people request to sit upstairs the best chance of getting an empty seat next to you will be downstairs.

Cheers,