As Mentioned above: Forget level! The boat hull needs to sit level on the trailer. the bunks are adjusted to contact and support the hull along their entire length (or as much as possible) with the hull level on the trailer. If they need to be tilted to do this, then that is what the trailer/hull combo needs.
As far as fender clearance: The only thing that moves is the axle on the trailer when travelling. As long as there is sufficient clearance between the hull and fenders, the boat will not move enough to do damage. It doesn't matter if the hull is between the fenders or above them. Look at the photo in the above reply.