Detonate once bubbled...
Some things that really helped me with my camera focus was to:
(a) Turn on Full time AF
(b) Leave my camera in Macro Mode (flower mode)
I had a real hard time with exposure, so maybe someone could help you with that. I often times had bright almost white water or Turquoise water background, with a dark, almost black foreground. I still haven't figured that one out.
With your internalf flash, leaving the camera in macro mode is right because the light isn't going past 3 ft or so and you'll be shooting within that area anyway.
I had a hard time with setting exposures manually, it was just sort of a crapshoot most of the time. The I picked up on something that cleared it up. The aperature (f/stop) is what controls your depth of field (DOF), how much is going to be in focus from front to back. The exposure time (shutter speed) controls the background. For instance if you have a scorpionfish on a hunk of coral with more coral in the background, you aren't going to be able to see him....he'll blend in with the background. You need a dark background, so use a faster ET, say 1/600. The 'shutter' is moving so fast that ir only has time to capture the light as it reflects off the scorpionfish, but not off the coral in the background. It's not that the light didn't get to the background, the shutter was just to fast to capture it. Make sense? And since the scorpionfish is positioned lengthwise, you're DOF doesn't have to be very much as long as you get his width in. So a F/8 or F9 would work well, you want to get a little bit in front of him in focus.
Aperture = DOF (what's in focus
Exposure Time = how fast the 'shutter' is open to capture the light.
Hope that didn't totally confuse anyone!