Move the Mods Folder

I use system links, or mkLinks in the CMD window. Orginal info from HowToGeek[www.howtogeek.com]

As Sins of a Solar Empire loads all of the needed assets on game start, this will not affect performance. If you are moving from a SSD, it may slightly change the load time.
This tutorial is for Windows 7, Vista will be very similar.

Cut you folder from the original path, mine is ...

C:\Users\myfist0\Documents\My Games\Ironclad Games\Sins of a Solar Empire Rebellion

Paste the folder in the new drive, my extra drive is F:\ so my new mods path looks like ...

F:\Sins of a Solar Empire Rebellion

Now, the game needs to looks for your mod path in its original directory, and the folder is no longer there, so we will fool it into thinking it is there with an mkLink.

Open the CMD window

Start --> Run --> CMD

or

Start --> All Programs --> Accessories --> Command Prompt

An Administrator privilege is required. If you are not on an Admin account, you can right click the icon shown below and
"Run as Administrator"

Edit the line below to suit your paths, first path in quotes is where the mkLink will go, the second path in quotes is where the folder is now actually stored (where you moved it).

mklink /J "C:\Users\myfist0\Documents\My Games\Ironclad Games\Sins of a Solar Empire Rebellion" "F:\Sins of a Solar Empire Rebellion"

You can manually type this line into the CMD prompt, or paste it in and press enter
(right click > Paste. ctrl+v does not work).

Once you have pressed Enter you should see the CMD window change to ...

You should see "Junction created for..."

Now you should have a mkLink in the original mod paths folder where the game can look and find your mods.

http://steamcommunity.com/sharedfiles/filedetails/?id=226860243#174120