You'll want to go into your install directory C:\ProgramFiles\Stardock\TotalGaming\GC2\Twilight (I believe that is the default directory, mine is actually installed in a strange place ) . You want to then creat a new folder and name it Mods. Unzip your mods into it. Once in game go to options and x the use Mods box. Below where it shows the directory hit "Change". If you don't see your mods in the popup box, just hut the default button which will reset it to point at your mods folder if it isn't already. Your mods should be selectable then.

This is how I did it though I'm not sure if it is the only way. I think I heard you can get the game to create the folder for you, but this is just as easy.

Another note since you mentioned getting multiple mods. You'll only be able to use one mod at a time unless you combine them into a common folder. It is as simple as adding the contents of one into another, but there is a catch. The Mods must not have conflicting files. If they both are trying to mod the same thing in a different way you'll end up with issues.

Examples I've used together are Kryo's Hull Mod, Carbon UI Mod and Evil Arcitecture Mod. As you can tell from the names they mod totally seperate areas of the game and therefore have no conflicts. Now if I was using a total conversion mod that had it's own UI and Improvements, I would have issues with using Both the Carbon Ui and Evil Arc mod with it.

Hope this helps some. There is some great mods out there