For integration with Steam (the overlay), all that matters for registration is the base game, registering the expansions has no gameplay effect.
You can register as many expansion through steam as you want and those expansions will be downloaded by steam automatically, but you can also install them directly.
I believe I only have the base game and the first (or maybe first two) expansions registered, all the rest I simply pointed the installed to my steam folder and it's worked flawlessly.
Note that if for some reasons you verify your Steam cache, it will delete any expansions you have not registered, but that just means you have to find the installers again, it does not affect the game once it is running.
D.