I bought the Galactic Civilizations II Ultimate Edition on CD from Amazon.
Here's what worked for me.
When you put the CD in, you will get a pop-up asking if you want to do an Express Install, Advanced Install, or Ignore. Ignore. Neither Express nor Advanced Install from the pop-up worked for me. Instead, from the Crossover Games menu, I selected "Install Unsupported Software." I created a Windows Vista bottle, and I manually selected the installer. I chose the setup.exe. Apparently the autorun.exe was the problem because setup.exe worked just fine.
Partway into the installation, I got an error message:
impulse.exe - .NET Framework Initialization Error
c:/windows/microsoft.NET/Framework/v2.0.5072/mscorwks.dll could not be loaded.
In case it messed up the install, I ignored it. When the the install went to 100%, I clicked "ok" and that got rid of the error message and the game finished installation.
The game crashed when I tried to load it from the regular icon, so I used the RUN command in the Crossover Games menu, selected the bottle and then selected GalCiv2.exe from the Program Files folder and ran that.
I got a whole bunch of error messages but just clicked through them. The game started up beautifully.
Still some of the minor yellow fonts are garbled at this point. I'd love to work that out. Also, the game crashed pretty quickly because I didn't fix the resolution (as mentioned here and in the tips&tricks section).
If anybody else comes along with the CD version, I hope this will help you get your game going.
Thanks also to all the people here who helped me get my copy going.
UPDATE***
Font issue: I went to my home PC (running XP) and copied the fonts from the c:/windows/fonts folder. I then went to my mac. I right-clicked the icon for Crossover Games, selected "show package contents" and selected contents/SharedSupport/CrossOverGames/share/wine/fonts and pasted the windows fonts. All my garbled fonts in GC2 are no longer garbled.
Crash issue: Every time I tried to load a saved game, it crashed. If I messed with the screen resolution settings in the GC2 menu, it crashed more often, even in a new game. The more I tried to fix it, the more it crashed.
I reinstalled. This time, from the Crossover Games menu, I selected "manage bottles", I then selected the bottle for GC2, then "control panel", then "winecfg" and "launch selected item". From the "winecfg", I clicked "graphics" and checked the box "Emulate a virtual desktop". I then followed the tips and tricks and entered my screen size minus 22 pixels for the menu bar.
I don't know 100% if I solved the crashes (perhaps not), but for the first time I was able to load a game without crashing the program, so at least I've made progress.