Hey Dustin,
You are certainly focusing on an important issue. Everyone knows that lights are needed but you rarely hear discussions of lighting placement underwater while it is always a major subject when shooting topside. Not sure what light arm you are using and everyone has their preferences. Some use the ultra light arms while others, like myself, prefer the loc tight arms or arms similar to them.
One thing to make sure of, and this can be affected by the port you are using and how wide its angle is, is to avoid placing your arms/lights too far forward as they can sometimes get in, and thus ruin, your frame.
I have not used the 4000s but have been told by other users that they have a nice diffused light. However, if you see that there are any hotspots, try separating the two lights so that the diffused edges slightly overlap rather than have both aimed directly at the subject. This will provide a nice spread of light and avoid hot spotting.
If you have a 3rd light, you can place it, unseen, behind a subject or reef for some nice backlighting effects as well. With two lights, you can position one aiming down from above the subject while using the spread of the second light more directly. This would be useful in medium or macro shots.
Remember that even the best of underwater lights have limited throw in the water, often only a few feet, so for really wide angle shots of reefs or things in the distance, your lights will be of little use.
While everyone has there own working preferences, if I see something I want to film, I will generally turn on my lights and get roughly the position that I think I will need before I settle down in front of the subject to film. Settling down first and then turning on your lights can often frighten your subject as opposed to gradually bringing them into play.
I'm sure others here will have much more to contribute as well.
Steve