I've been hauling 'toons for years on top of my Jeep. The boat I'm using now is a bit wider than the standard rack but that doesn't stop me. I just strap it down on all four corners with the quick-straps canoe and kayak people use.
The Dry Fly boats mentioned earlier come from a great guy with great customer service but I just couldn't get past the high profile of them. The windage that must cause, not only when it's windy on the water but at 80 MPH on the freeway? No thanks. I don't like sailing when floating and sure don't like buying extra gas for the Jeep to make up for the drag of a boat like that.
For getting my rig up on the Jeep my buddy came up with a really clever idea.
The carpeted boards below are hinged in the center for storing. I lash the ramps to the roof rack with the same straps I use to haul the 'toon on top of the Jeep.