Parallel or perpendicular?? It depends on the 1) shape of your tank, 2) the spacing of the bulbs, and 3) the type of reflector you will be using.
FWIW, I found that the parallel positioning of my fairly closely spaced (16") 400watters was throwing a lot of light onto the front glass of my 36" tall tank (the plan dimensions of the tank is 78" x 32"), which was decreasing the clarity of the glass (I have 1" laminated glass, which is sensitive to light refraction). Turning the bulbs perpendicular improved the situation by reducing the amount of light on the front glass and by giving be a more consistant level of lighting across the tank, enough so that the tank is well illuminated by only 2 of the 4 bulbs.
The downside is that turning the bulbs perpendicular means that your canopy will end up being fairly deep (front-to-back). Moreover, if you are going to supplement with actinics, then these bulbs will be pushed fairly close to the front and back of the tank (unless you are using short, perpendicularly oriented PC's).
As to height, good reflectors should reduce the impact of this variable. In other words, placing the bulbs at a heigth sufficient to dissipate heat (8"-10") should be fine if your reflectors are still directing the majority of the light back into the tank. Increeeasing the height of the canopy will help achieve this.