It is very simple...it is programmed when the engine is not running but the key is in the run position and the tranny is in drive.
As per the site, a number of the tw positions controls a certain parameter. If you want to change the default cruise number, you put the tw on pos 5, key on, engine off, tranny in drive, and read the current number in the cruise fuel program in the blm slot of your scan tool. If you want to richen the cruise number by six, you pump the gas pedal six times. If you want to go leaner by six, you switch the ac on, and pump the pedal six times and the blm read out will drop six numbers...go back and read the site, it is pretty clear.