You should see some major differences in the tech trees right away. The mod probably is not loading. Verify the mod path is correct in prefs.ini located in the My Document\My Games\GC2TwilightArnor directory. Also verify that "Use Mods" is checked in the game options menu. Verify the contents of the Marklar directory. The paths must be correct or the modded trees won't load. Reference the README.txt file in the zip archive.
Hope you get it going and thanks for giving it a try.