Really the only way to choose a frequency is to step through frequencies on your car radio, until you get a clear slot (ie, where all you hear is white noise - with no radio stations). Then tune the iPod/iTrip to that frequency.
Having said that, I've found with my FM transmitter (not an iTrip, mind you), that the best frequency overall seems to be 88 MHz - there doesn't appear to be any station on that frequency, wherever I've travelled in the country.