I've been researching info on this very topic, and found a video produced by ShipShape TV. Although this video is about a specific product, the narrator mentions that wooden stringers should not be touching the hull directly (that part is towards the end of the video):
http://www.youtube.com/watch?v=8Muf7G3T7Z8
As RidgeRunner already mentioned, the bedding compound serves the purpose of keeping the stringers off the hull. I like the idea of putting small spacers (kinda like shims) between the stringer and hull before bedding it down. That would prevent you from accidentally pushing the stringer too far into the bedding compound. What kind of thickness would be appropriate? I'd guess 1/16", or would you want as much as 1/8"?