What most likely happened is that your extraction program created a folder with the same name as the archive and extracted to that. However, the mod already includes its own folder, so that got extracted to the folder that your extraction program created, resulting in the nesting that you described.
To fix this, move the nested FEP folder (in this case, the one without the version number), to your FS2 folder. Then, delete the first FEP folder (the one that you didn't move).
Don't worry about the lack of a version number in the folder name; most mods that include their own folders don't include one there.