Sins of a Solar Empire is a bit weird in how you install the mods, you don't put the mods into the game folder. There is a separate folder stored in your My Documents/My Games/Ironclad Games/Sins of a Solar Empire/Mods-Rebellion-1.82/mods where you place the mod. Be sure to run the Large Address Aware.exe and point to the Sins of a Solar Empire executable. Sins needs to be modded to become Large Address Aware otherwise you run into memory issues when running Star Trek Armada III. I hope you have more than 4GB of RAM otherwise that may be a problem for you.
