You may want to look at the response characteristics of your set of omnis to see if they are truly flat or have peaks at some of the various frequencies. My Gefell omnis, for example, have a high-frequency bump at around 10,000 hz. making them better suited for recording at a bit of a distance. Other omnis that I have seen are flatter, so they may benefit from being placed up closer where they can capture more direct sound and not be as affected by room resonances.
In my experience, 3' is too close for omni spacing. I prefer a slightly wider spread of between 4' and 6', but that may just be personal preference. I have run at 10' before and didn't like the results too much; it sounded like there was a hole in the middle of the soundstage. Experiment with what you like best.
As far as directionality, I point the capsules at the stacks to better capture high-frequency responses and midrange. I don't know if this is a placebo effect, however. As the capsules are supposedly "omnidirectional," I really don't see much benefit or harm (in theory, at least) in having the capsules at 180 degrees or the like.