You're not missing anything. All the options it asks you for can also be found in the normal mochaAE prefs. It just asks you whether or not you want to use accelerated drawing functions and where to setup its default storage folder, but that is nothing I would consider essential, as it can be chnaged any time.
i just installed CS5 master edition and i can't find and start Mocha. i know it might sound dump but i cant find mocha help plzzzzz
Mocha is a stand alone program that you'll find in the same folder as After Effects. If you still can't find it just search your system for a folder named Mocha.
If you have installed the demo version, you won't be able to use it BTW. If you have a registered version, you already have the answer above
Hope that helps,
Corrected a typo