There is no version 2.0. There is, however, a v1.2.
Mods may or may not be designed for the new mods system in 1.2. If they are, you need only unpack them (assuming they're properly set up in the zip) into C:\Program Files\Stardock\Totalgaming\GalCiv2\Mods. Then when you run the game, go into options, check the "Use Mods" option, click the "Change" button below the Mods directory box, and pick the mod you want to use from the dialog that pops up. Restart GC2 to apply the change.
If the mods are not designed for the 1.2 mod folder system, read the readme, mod description in the library, mod thread, or contact the mod author for more details. Or at least tell us what mod it is so we can help.