The ideal Canon set up for macro photography is:
Canon 100mm macro lens
(at least) one, but preferrably two Canon Speedlites (flashes), the 580EX is the best.
Canon STE-2 wireless transmitter
Camera settings range will be f/16-f/22, and shutter speed of around 200, ISO 100.
VERY basically you are positioning one flash over the subject (directly) at (generally) full power. The second flash is hand-held and serves as a fill flash, so it is (generally) powered down a few stops (less flash brightness than the overheadf is the idea). That's why the STE-2 is used-- it will fire both flashes wirelessley, so you can easily move them around, etc. Though you could have them tethered, the STE-2 is considered "essential" by most serious Canon macro shooters.