The place for adding autonomous code is in User_Autonomous() in user_routines_fast.c, under the comment
/* Add your own autonomous code here */
It will be a good idea to make an auto.h/auto.c to have all your autonomous functions, and use user_routines_fast.c to call a central function (auto_main() perhaps).
Anyway, look at
http://kevin.org/frc for lot's of more cool information.
[edit] Also, look at
http://www.ifirobotics.com/docs/lega...2-apr-2004.pdf too. This is last year's programming reference guide. Most of hte things there still apply. Obviously though, you won't find any references to the camera there. (and don't bother about references to the line tracker, which was "last year's camera"). [/edit]