Hi Brett,
I'm using a similar system a Canon A70 with the Canon case. Here are some pointers.
I've been looking around this site for a couple of hours now and so far I have found out :
I should be setting my camera to iso 100 or slower.
I should always use the difusser with the built in flash
Try to get within a couple of feet from the target.
Here's what I would like to know more about
You should use ISO 50 when shooting with flash, you will get less noise.
It's true it's best to use the diffuser when shooting with the internal flash but you can take good pictures when you're in shallow water without the flash. When you're are deeper you can do interesting thing without the flash but you have to think that your camera is loaded with B&W film.
When you are within two feet remember to use the macro mode
Can anybody point out some good articles or tutorials or have any tips for my setup?
This Canon site is very good for people who are beginning
http://www.canon.co.jp/Imaging/uwphoto/index-e.html
You can also pay a visit to my site where you will a few tips for a Powershot setup.
General base settings for 1st dive. I was thinking of using TV to select a shutter speed of around 1/250 and turning the flash on to prevent shake.
When using Tv with the flash the A80 will default aperture to f/2.8 if it reacts like my A70. It's OK if it works with the ambient light. If you have too much ambient light the best approach would be to go manual with 1/250th (1/500th is supposed to work too) and reduce the aperture.
Tv is preferable to Av when shooting with flash because the A80 will default to 1/60th in Av with flash and you will (or may) get some movement blurring depending on water movement and your bouyancy expertise.
When you shoot macro try to find a busy background so that the diffusion specks will blend with the background. The internal flash is really close from the lens!
Use the sunlight settting when shooting flash and the custom white balance when shooting ambient light. If you're too lazy to use the custom white balance, at least use the AWB so that reds won't be eliminated from the JPEG.
Set the "Effects" to OFF, use the largest resolution with least compression.
You were asking about "Natural light vs Flash", my advice would be "try both!" If you're shooting macro try to use the flash but sometimes it doesn't work properly and dumps too much light.
Shutter Speeds how fast to prevent shake? I dont have an underwater tripod!!! (yet)

1/125th may work if you're not using the zoom. BTW try not using it and get closer instead. By all means shut out the numerical zoom. 1/250th is almost always OK. If you want to avoid the shake and get a shorter shutter delay try depressing the shutter halfway to force the camera to find it's focus and fine tune the framing afterwards. It's tougher on moving subject but if you anticipate the distance at which you will shoot the subject and prefocus on a static object at a similar distance it works. This helps me to reduce the shake because I have a tendancy to press harder on the shutter when I sense the camera is not taking the picture.
Can you take seascapes of corals or do you always need to be close?
Of course but be sure to custom white balance. Look at the POTW Winners #31 for an example taken at some distance of the subject with a Canon A70.
Is the camea's "visibility" the same as mine?
I'm not 100% sure about what you mean but if you're talking about the optical viewfinder, you will soon find that you're framing with the LCD.
Oh! and one final word of advice...get closer!
So where are you going diving?