for the mods folder on vista/w7 it should be c:\users\"user name"\Local Settings\Application Data\Ironclad Games\Sins of a Solar Empire\mods

for xp it should be C:\Documents and Settings\"user name"\Local Settings\Application Data\Ironclad Games\Sins of a Solar Empire\mods

if you do not see the mods folder with one or more folders with the name of the mods in the folder name then the mod were extracted to the wrong location.

if you only see rar files then you need to extract the files with either winrar or 7zip

ditto for zips or 7z files

harpo