Hello Lawrence,
regarding WC - WC II differences, they are (I'm going by memory):
- blue sticks
- more robust tall switches
- 4 three-position switches (very nice...)
- 1100mAh default tx battery
Regarding software ones, they are minor (at least for airplane models). For airplane usage, only one function for in-flight mixture control is the new addition. I don't know for hely, but here you could find everything you want:
http://www.futaba-rc.com/manuals/manual-9z-notice.html