Basically, the whole installation process for Impulse is screwed up. If you are downloading the files, and don't choose to have it ask you, it will (theoretically) install the GalCiv2 stuff to where you have specified in Impulse (in Preferences - Folders, then what you have in "My Games" in the "Install Location" pull-down). And THEN it will append \Stardock\TotalGaming\GalCiv2 to the end of that.
Whether Impulse at any time is smart enough to look at registry keys or prior installations to choose a better path is unknown to me at this point. That's just my experience from running the install one or two times by downloading, plus restoring an Impulse archive (where it NEVER asks for the location, even if that box is checked in Impulse).
I have not run nearly enough tests to be sure EXACTLY what the darn thing is doing in every instance.

All I know is that to be sure the darn thing works, the best thing is to leave the all the defaults, and install ALL GalCiv2 stuff from scratch with Impulse. This will make ensure everything goes in same directory structure (C:\Program Files\Stardock\TotalGaming\GalCiv2, and DarkAvatar and Twilight folders will get created below that) and all registry keys are created.
Which is a pretty bad solution for those of us who have multiple drives and partitions.
-HM