If you are really out for Cd having your passengers in tandem would go alongway towards that.
Then your design could be more torpedo like, lol.
Seats low slung angled somewhat heavily backwards( I think you wanted rear wheel drive? that might not have been something you were looking at) and the engine could be mounted behind and a little under the second seat.
Cooling you could use small fins on both sides like the Bentley Speed 8.
http://members.fortunecity.com/freec..._speed8_02.jpg
You would want to angle them so thay are pulling air from a lower point to a slightly higher one to increase downforce on both sides. OR instead of using it for cooling you could ram-air if you wanted to go that road.
The original designs for the Speed 8 called for the rear-view mirrors(side view mirrors) to be mounted on the wheel guard and the front to be slightly more tear than it is(which would put the fairings on the front right tire higher than the rear ever so slightly).
I would go with Tandem for coolness sake let alone the potential enormous gains you in Cd you might be able to reap from the much decreased frontal area and potential stability.