I like the fan to be over the bed. It is the most effective there, and you can access the controls without getting out of bed.
came with a Fantastic Fan which has worked flawlessly. On high speed there is significant wind noise, so we run it slower when sleeping.
We also added a Maxxfan canopy so we could leave the fan hatch open in all weather, and when under way. The Maxxfan cover is well designed to mount to the Fantastic Fan, and be quickly removed for cleaning by removing some pins. The grill has 3 sides (facets) that increase the total area which passes more CFMs of air. It is a very well thought out product.
I wouldn't worry too much about waterproofing, as most all trailers have these types of penetrations. If your roof is concaved and holds water, it may be preferable to install a glassed in curb to get above the waterline. Ponding water is hard on caulked joints.