Good Tips Tassie and everyone, but I disagree you want to force the internal flash on with his, and mine, set-ups.
The battery life of the SP-350 can be extended by not using the internal flash, as he has the ikelite housing and DS-125 he's using the TTL cord.
I shoot in manual mostly, and you'll learn your rig after a couple of dives, Experience is everything, you just can't learn this stuff by reading a book. TTL metering is also good, so play around with it.
It also depends on the look of the photo. Are you shooting flat over a reef looking into the distance? and say you want a blue water background, or black background. Well if you slow the shutter down to 1/60th-1/125th, you abosrb more light and it'll be a great depth of field and go off into infinity, but say you're shooting the same Gorgonian sea fan with a crab on it, and you want a black background, go to a higher shutter speed such as 1/1000th, and higher strobe power and you illuminate all close up colors but the background is matte black.
I set my white balance to cloudy, I'm too busy underwater to set it manually. Depending on water clarity, start with ISO 200, but I also set it down to 64, or even 800 for deep dives.
The key is THROWING LIGHT.........if you're in macro, you don't need to blast full power and wash out colors, but if you're shooting with a wide angle lens from a distance, shoot at a slower shutter speed and higher f-stop.
practice practice practice. I can easily shoot 100-120 photos during a dive, of which I'll show off 10-20 keepers to friends. During surface interval, swap out a new 1 gig mem card and fresh batteries. Shoot in Video mode too (white balance in cloudy mode) while using your DS-125 internal modeling light, this works great even during night dives.!