It should install right over top without any complaint, though if you prefer to keep it clean and do an uninstall, doing so shouldn't remove any settings, saves, or ship designs you have (though those won't be portable to DA/TA).
Thanks for the info.
One more question, should I leave my curent GalCiv II serial number in Impulse, or remove it and register the one that comes with the Ultimate package?
Edit: If you have the Ultimate edition installed, can you choose to play just the base game, or with just certain expansions?