You're going to want to get close, whatever settings you use if your waters are dark!
If you are only using internal flash, then this is one of those times when you are going to have to figure out which sacrifices you are willing to make as you won't be able to use the same settings as those in clearer water for a lot of shots.
When you are close enough to your subject that your internal flash lights the whole scene, then all the settings you have seen around the forum should be a good starting place: ISO 100ish, f4.5 or higher (I like f8 when I am really close to stuff!) and shutter of 1/100 or higher. REember, all your light is coming from your flash in these shots. This is going to give you the best colour and depth to your photos.
For those shots that are farther away, you are going to need to bump up the ISO to 200 or 400 and/or open up your aperture and/or slow down your shutter speed. Dropping your shutter invites unwated movement and blur; opening your aperture may give your photos a "softer" feel, even if they are in focus; upping the ISO may cause more noise to be visible in your photos.
It's going to be a matter of experimenting (settle in for a test session - shoot the same scene at a variety of settings then compare on the computer...delete nothing underwater!) and finding which settings work best for you!
Please let us know as there are quite a few divers up there - hopefully some will chime in with what they use to get you on the right path!