Re: Fly orientation.
I would echo Dan's sentiments. The fly should be tied in the manner in which you want it to "swim". For example, a Clouser is tied to ride hook point up therefore if you tied it olive over white, you would want the white to be on the weighted side of the hook to imitate how a bait fish would swim.
Conversely, a wooly bugger doesn't necessarily have a "side" since it pretty much looks the same. I tend to use dumbell eyes rather than cone heads or just lead on my buggers because I like them to ride hook point up. For non-weighted flies you can also achieve the same thing with a "wing" to flip the fly like many bonefish patterns are tied.
At the end of the day, much of it depends on how you want the presentation to look and in what conditions you are making the presentation.