OMG!
Modding 101. LOL
@Steamwake.
Your MODs are arranged in JSGME by the order they were enabled. So find the corresponding folder for the MOD (by default in the MODS folder) and copy the Commands_en.cfg file. This file will be the last activated version of the commands cfg and therefore the active one.
@ Both of you.
A JSGME File structure is as follows:
Name of MOD > data > cfg > Command_en.cfg
Name of MOD > data > Textures > TNormal > SpaceStationMoon
Name of MOD > data > etc etc........
See the pattern, Name your MOD and then just replicate the folder structure (or path

) to the original files home. Pop your MOD into JSGME's MODS folder and enable.