Great question, you can install either a roof top mount or under bunk air conditioner although there are a few pros and cons of each unit in your application.
Firstly, the roof top installation will be more time laborious as a hole has to be cut in the roof, 240-volt power has to be run and a H - frame will more than likely be required for structure and rigidity. There for the labour factor will be higher than having a under bunk unit installed and will be costlier on the hip pocket. Installing a under bunk unit is more cost effective all though you will lose a minimal amount of space as the under bunk is installed under your bed or dinette seating arrangement, under bunk units are usually a little bit more expensive than roof top units so it will all boil down to the owner's personal preference.