It'll be the weekend before I can give you anything really in-depth. But Jonesoft will create a folder within the Orbiter root path titled "MODS", inside this folder is where you would have sub folders for each mod.
(example)
-mods
+CSSC
+Energia-M
+WideAwake
+XR-5 Vanguard
Jonesoft has an icon to double click that will open a dialog that is pretty intuitive. Select the mod you wish enabled and press the [->] button. Run Orbiter and hit the skies.
If you add something that 'breaks' or causes a CTD, you can easily drop out the last mod enabled to see if it is the one causing troubles.
If I were to disable every mod that I have, I'd be left with Orbiter, with only SC3, MS2, DGIV, UCGO and Sound.