There are so many possible combinations of "settings" with an S90 and a D2000 strobe we need a little more information.
I doubt whatever "settings" you got from Ikelite are correct for the D2000 strobe.
In all suggestions below, camera strobe will be set to ON or Forced.
Shooting in Av mode:
Camera flash set to manual under Menu and power level to low, this will conserve battery power and eliminate pre-flash. D2000, install magnet in switch, set strobe to External Auto and simply match the f stop selection from the camera to the strobe power knob. Under or over expose by increasing or decreasing strobe power with the knob or setting a different f stop in the camera than in the strobe etc.
Program (P) mode:
S90 in P mode, D2000 in sTTL mode, magnet position is irrelvant as the selection of sTTL mode overides. On the S90 selection of P/A also overides your previous "manual" strobe setting in Menu. Increase or decrease exposure via the D2000 power knob, shoot mostly in sTTL normal or low.
Manual Exposure mode:
S90 in Manual exposure mode, camera strobe power under Menu set to lowest, set the D2000 to Manual mode and match f stop on the strobe to that on the camera, bias exposure by f stop setting different from the strobe or strobe setting different from camera.
Other stuff:
Camera set to ISO100, Use the cloudy or underwater mode in the selections or shoot RAW plus jpeg for post process color correction and/or use manual white balance.
Strobe need to be close, no more than three or four feet.
You need a wide angle lens under water unless you are shooting macro so you can get CLOSE! You must get CLOSE!!!!!!!!!!!!!!!!!!!!!!
Remember, set exposure for the near ground and subject with f stop and strobe, set exposure for background with shutter. A slow shutter will give lighter backgrounds, a fast shutter will give a darker background.
The above are not, NOT, the only possible combinations, they are basic starting points.
In your camera, go into Menu, set strobe to Manual and lowest power, turn the IS to shoot only, turn off all of the Safety Focus, Safety Exposure crap, turn offf the focus assist light, set Power Saver to leave the lens extended and the screen to go Off, this allows the camera to wake up with a button push. Set the meter to Center Weighted or Spot.
Turn on the Histogram and the Focus window to help you see Focus. Use a half press to allow the camera to focus. Do not use Auto mode, it sucks.
Use the diffuser (EA type, blue minus 0.5 is technically correct for the S90) on the D2000. Use the optical cable.
A wide angle lens is not really an option underwater, IMO, it is essential. You MUST get close to your subject. A strobe is only good to about three or four feet, at the outside five feet.
You must shield the camera flash so that it does not cause reflections from direct lighting on sediment in the water.
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