And people were saying that this place is dead. :rolleyess
As Rhett said, the level-select screens are self-explanatory.
As for mods, just unzip the zip files, and put the mods (___.gob) into Patch Commander (it should appear as a folder marked JKPatch
in your JK directory). Then run Patch Commander, and click the mod in the menu, then hit the "Play JK" button.
Patch Commander also has Mysteries of the Sith
support, but if you don't have MotS, then that's irrelevant.