Could it be that the software you are using to unpack the archive has created a new folder named after the file itself?
Just hitting "extract archive" is a BAD IDEA. It is better to open the archive using winzip, 7zip or winrar and then manually extract the content.Okay, please read and follow these instructions carefully:
1. Please check if there is a folder with the same name as the archive - "Mirage_Battleship_Gray" (I assume that is the "file" you are talking about). If that is the case, open that folder.
2. You should see three folders within this one: Game Data, Images, Models. Select all of them and hit ctrl+x.
3. Exit the folder and go to Star Ruler\Mods\galactic-armory-1.9.4\. Click on an empty space or any file within that folder and hit ctrl+v.
4. When prompted to overwrite files, select "yes" or "overwrite all".
I know Star Ruler involves space ships and stuff, but this isn't rocket science, trust me