Hopefully the above settings I posted will help out a bit.
The night shots will be very difficult to get right because of the low light, you can turn up the ISO a bit for them - but the more you turn it up the more "noise" you will get on your pics - and this will get ugly especially if you start adjusting brightness/colours in photoshop.
I would try and avoid the flash as much as possible as it usually just leads to ugly shadows, over exposure and de-saturation of colours. If you want though, try and be creative with the flash, eg: slightly cover it with your hand/finger, or cover it with tights (ah tights, what would us fishkeepers do without them!) - basically try and diffuse the harsh flash light.
Again, the best way to get your night shots is with a tripod and a long shutter speed, but with such a dynamic subject like corals this might be very difficult to achieve.