1. One of the biggest things you can do is to make sure that the camper portion that goes over the truck cab follows the slope of the windshield. Or that it does not stick out beyond the front of the cab over the front windshield and that a fairing can be added to create the same angle up as the slope of the windshield. So many campers have the over cab extension that go beyond the front of the windshield, talk about an air dam. Might as well deploy a parachute and drag that around. So if you (a) leave room for a fairing to match the windshield slope or (b) design the slope into your camper - you are way ahead. I would say that would be about 20%-30% of your optimum achievable aerodynamic design. If you have that overhang, you are just about screwed.
2. Make that roof convex. Akin to this camper pictured here.
http://xtrv.smugmug.com/gallery/8908475_XhKRb#591112274_qNHwE If you don't design it convex, then plan on designing a round roofed rack perhaps. What would amount to a bolt on rounded roof rack 'fairing' making the roof round.
3. design a short, easily collapsable boat tail. Something that can be bolted on and might take 15 seconds or less to get out of your way when you need to access the back or get into your camper. Akin to this
http://www.roadtransport.com/blogs/big-lorry-blog/2010/06/post-15.html
Almost any camper design can be made into an aerodynamic shape after it is built as long as you take into account that you will be adding fairings to make it so afterwards. But not if you have that forward overhang above the windshield, nothing can be done about that once it is there.
Point being, that you can build your camper and then make it aerodynamic afterwards with proper design planning now.
Even the vertical protrusions behind the cab above the bed on both sides can have short collapsable fairings installed.
And what sort of truck will this camper be going on? I can't reload the thread right now for some reason to see if you mentioned it. If you are starting with a truck that gets super bad fuel mileage already, then you most likely will not be happy with any results you get.