Dragon in Flight
Originally uploaded by Dalantech.
Some of the setting info you asked for does come with experience -and it really depends on your shooting style. But here's what I use, and keep in mind that I don't use a tripod or a monopod.
For closeup photography (1/4 to 3/4 life size):
Shutter priority 1/400 with the ISO set to 200 - 800 depending on what aperture I'm getting with that shutter speed. I try to shoot no lower than F5.6. Normally I'm in shutter priority if I'm trying to freeze a little subject motion.
Aperture priority F5.6 to F8 with the ISO set to 200 - 800 depending on the shutter speed I get with the aperture setting. I try to keep the shutter speed at twice the 1/focal length rule. So if I was shooting with the 100mm I'd want my shutter to be no lower than 1/200. Great for when I'm trying to control the depth and there is little to no movement in the scene.
A flash can be used for both of those settings for fill light to bring out more detail in the subject, but set the flash to -1 1/3 to -2 FEC and diffuse it. You want just enough light to fill in the shadows a little, but not so much that the resulting image looks like it was taken with a flash...
With few exceptions (like low depth of field flower shots) I shoot in manual mode F11, 1/250 (the max sync speed of the Canon 40D) and ISO 100. At those settings when shooting at life size or higher magnification that flash will be the only significant source of light in the scene so the shutter speed is irrelevant -the duration of the flash is your shutter. the key to getting sharp images when shooting macro is to diffuse the flash and get it as close to the subject as possible. The closer the flash is to what you are shooting the shorter the flash duration will be -your "virtual shutter" speed will be extremely fast and you can freeze a lot of motion.
Any flash will do -just get it off of the camera and out toward the end of the lens. If you get a macro flash then I'd recommend the MT-24EX over the MR-14EX simply because the MR-14EX's flash heads are too close to the plane of the lens -getting good shadows, even with ratio control, is difficult. Using the flash mount that Canon supplies with the MT-24EX you can get the flash heads far enough from the lens plane to get good shadows and once you find a way to diffuse it (plastic from a milk jug works wonders) you'll get some really good light. I've never tried it, but you could also cut up a Lumiquest Soft Screen and use it as a diffuser.