Version 1 is the most tested and currently used.
Version 2 is new, prints easier, is smaller and uses less hardware. It is currently only compatable with the PCB.
The inserts and knob_cup_v2 work with both versions of the hardware. You'll need prints from both of those folders no matter which version of the case you decide to use.
Don't be intimidated. There's a growing amount of customization, so the folders are here to help. In general you'll only need one .stl from each directory, with the excepting being the gears. There's additional information in each folder to help you determine what part might work best for you.