Manual focus is best for accuracy on macro photography, but since you want to know about auto-focusing, here it goes:
1. Turn the AF/M switch on the lens to AF (this is very important)
2. Activate auto-focus using "C. Fn. III-06 AF During Live View Shooting. Choose to "anable" this feature (in the Menu)
3. Press the AF-DRIVE button and use the Main Dial to make sure the auto-focus mode has been set to One-Shot (on the LCD screen)