If I understand your question, you want to know where the Mods should go?
For my HDD, it is C:\Games\Steam\steamapps\common\galactic civilizations ii - ultimate edition\Mods
Look at your Steam shortcut properties and it should list its base directory.
The Steam browser should not really care about any mods you have, unless they are not compatible with the game and the technical mod requirements or requisites - but that I would not know of, as I have only been playing the game a few weeks, so I will mod it later on after a dozen or so games.
if you could be more detailed on 'your issues', i could append further advice.