1) There are infinite possibilities for setting up flash. You can actually get away with a hotshoe flash in the camera's hot shoe. Not the most interesting lighting, but if the lens is nice and close to the glass, you should be OK with reflections. . .I'm pretty sure I've done this before with acceptable results, but the lighting is just uninteresting. With a single flash, just get a flash cable, and play around with different positions. I'll generally keep it level or higher than what I'm shooting and offset slightly to the left or right. You can even come in from the side of the tank for very contrasty lighting. Another option is to bounce the flash into the top of the tank off a reflector positioned over the tank. If you want to get more advanced, you can use multiple flashes.
2) If you're using flash, you can usually shoot pretty low ISO. Aperture really depends on the effect you're going for. At fast shutter speeds and low ISOs, you're the background is going to be underexposed, so the flash is isolating your subject, and you can shoot with a high f-number (often f/18 or higher) to ensure the entire fish is in focus. Keep in mind that when shooting macro you have a relatively shallow depth of field. Lastly, your camera does factor the flash into your exposure. It uses a system called Evaluative Through the Lens (E-TTL). When using flash as my primary light source, I will either use manual exposure and let the camera/flash combination take care of the proper exposure, or shoot with both the camera and the flash(es) in manual. The latter takes some trial and error, since my hand-held light meter isn't exactly waterproof.
3) For flash in general, the big things you're looking for are power and control of your lighting. I'd definitely look for a flash that allows manually setting the flash power as well as automatic modes that allow you to set a Flash Exposure Compensation (FEC). As far as value, Canon's 430EX is a very good flash. Certainly not the most powerful, but should be plenty for most aquariums, and it allows full manual control. A step up from that is the 580EX, which is much more powerful and also allows IR control of other Canon flashes (like the 430EX). There's also a newer model (I forget the model #) that I believe has a radio transmitter instead of IR. You can also go with third party flashes to save some money. In the end, light is light, but you may loose E-TTL. Many will still have TTL, which is a less precise version of E-TTL. Don't be afraid to spend some money on a good flash, though. It's one of the most overlooked assets by new photographers, and when used properly, can do far more good for your photography than most other accessories (including lenses in many ways).
