I found when installing Mods I have to put the MODS sub-directory directly in the SOSE directory where I installed, i.e., J:\Games\Sins of Solar Empire\Mods. If I put in my C:\Users\kbrown.HOMESYSTEM\AppData\Local\Ironclad Games\Sins of a Solar Empire\Mods directory they do not get applied.
Not that I care where the files gos.....but have seen a number of posts where people do not see the mods as working.