Hi Gary,
We speak with many customers about their mud flaps, and hear all sorts of stories and opinions.
The most important step to preventing rocks from hitting your toad is to stop them in the fenderwells directly behind the tires where they start. You want to make sure those mud flaps are as long as possible without them hitting the ground when you let the air out and drop your coach. Usually they end up around 4" off the ground as you are moving down the road. Also make sure they are made of a stiff enough material to not just fly up behind as you are moving. These will stop at least 80% of the rocks.
Just like you do everything you can to get the best possible mileage, you may also want to do everything you can to stop the rocks from hitting your new tow vehicle. The mud flap across the back is just one more way to increase the protection. You do want to make sure the mud flap is not too close to the ground. We suggest at least 4" off the ground. Otherwise, on uneven and/or gravel roads you may actually end up throwing more rocks at your tow vehicle.
Some RV'ers also suggest using a shield between the coach and the toad. These are a bit cumbersome, but for a brand new vehicle, it may be worth it.