In terms of the funky colors, the main issue I observed is pushing a bit to much towards the red in certain reef scenes, which introduces a noticeable magenta color cast into the water column, too.
So if I understand correctly, you
1. Kept the camera set to either auto WB or underwater WB;
2. Did not use a red filter on the camera;
3. Did not use a blue filter on the lights; and
4. Did not do any color correction in post or increase the saturation in post?
What picture profile were you using?
Basically, I would not recommend using the underwater WB mode with the video lights, as underwater WB will set the WB too warm for subjects primarily lit by your lights. That could account for the red push in some of the shots. Auto WB or fixed WB (5500k) would work better for shots primarily lit by your lights.
In terms of exposure strategy, I would actually try to keep the lights on full power unless the ambient light conditions are /really/ dark. Basically start around F8, 1/50, ISO 400. I doubt your lights on full power would cause overexposure at such a setting. If you find that this produces a water column that is too dark, then raise the ISO and lower the power of the lights to avoid overexposing the foreground. If the exposure is too bright, leave the lights on full power and lower the ISO first. If still overexposed at F8, 1/50, ISO 100, start closing down the aperture further until F16, then start raising the shutter speed. I can't think of any conditions underwater where F16, 1/100, ISO 100 would cause overexposure from either the ambient light or the artificial light, even at midday in shallow water.