Vasari Admiral... do the following:
Start your desktop:
Create a new folder on a hard drive with enough space.
Call this folder "Rebellion 1.1. for Mods" (or something similar)
Start your laptop...
copy ALL Rebellion 1.1 files into the "Rebellion 1.1. for Mods" folder on your desktop computer.
DO NOT OVERWRITE YOUR CURRENT GAME IN THE STEAM SUBFOLDER!.
Games - "Add non Steam game to library".
Select the folder "Rebellion 1.1. for Mods"
Select the file "Sins of a Solar Empire Rebellion.exe"
Now you should have 2 Entries for Sins Rebellion in your Steam Library.You can even edit the name for the just created link... like Rebellion Mods 1.1 or so.
I hope that helps.