I would just connect a switch to one of the digital inputs and use that to control when the bot is in "autonomous" mode vs. driver-controlled mode.
Then just use an "if" statement:
Code:
if (rc_dig_in16) {
// Run Autonomous Code
} else {
// Run Driver Control Code
}
You could put this in the Process_Data_From_Master_uP() function found in user_routines.c. If you want to keep the default drive code, put it after the call to Default_Routine(), however you could nix the default drive code by replacing that call with your new code.