I think the assumption was that you would want it downstairs.
I cant see any reason why they woudn't install it wherever you wanted.
Swap the boxes over yourself before they come so that you have the new one downstairs and the old one being replaced with sky hd upstairs.
They have no clue which one was installed first, nor will they care.
This is assuming that none of your existing boxes are SKY+. That would complicate things a little.
all the boxes belong to you, they shouldn't be taking any away, and you can put them where ever you wish - the best one downstairs, the older one in a cupboard as a spare, or on ebay if you like.
unlike a cable company the boxes belong to you, and you are perfectly entitled to swap them or sell them on