Ok, if your running Vista the directory is as following: C:\Users\"user"\AppData\Local\Ironclad Games\Sins of a Solar Empire\Mods
Where you put "user" add whatever your user name.
If you try and find it via by exploring your computer you wont find the AppData folder due it be hidden by default. You can either enable hidden folder to be show up or just type it in.( I just type it it.)
Once you find the Mod Folder just unzip the Mod into that folder.
Next step would be start up SINS and go to options tab. In that tab there is an another tab call Mods. Click on that and if you unzip your Mods right they will show up there. Just click on the one you wanna enable and click on the enable button. SINS will load it up and you should be good to go. Note: You can only have 1 mod enable at a time.