When you shoot with flash you have two exposures to balance - the ambient and the flash - and you can control them independently. FEC for flash works in exactly the same way as EC for ambient. When you shoot with ETTL-II the camera does all the work, sending out a brief pre-flash to measure the light reflected back from the flash, calculates the power required for a "correct" exposure and then lets rip with the power it thinks is required. If you have the camera in Av/Tv/P mode and the flash in ETTL-II mode then the camera will try to balance the blend of light for you. ETTL-II flash metering is fooled by a predominance of dark or light tones in the scene, just like metering for ambient. Just as you can adjust EC for artistic taste or to compensate for an unusual tonal balance for ambient light you can do the same thing with FEC for the flash
Equally, when setting your ambient exposure manually the concept of EC disappears (for Canon) and if you set the flash power manually the option for FEC disappears. In both cases you are in control and you dial in just the exposure/power you want and the camera won't fiddle with it.
You do need to be a little careful with Canon's system if you don't know how it works. When I shot my first wedding I left the camera in Av mode and let the camera and flash do its thing. Pretty much every shot was underexposed and at times my slow zoom lens meant I was getting slow shutter speeds and evidence of blur in the subjects. Nowadays I set my ambient exposure manually and leave the flash to roam free using ETTL-II. However, it is important to evaluate the scene before you, chimp your shots and check your histogram to make sure you are getting the right results. Once you are dialed in then you should be pretty OK, and with the ambient exposure locked down you'll only have to worry about what the flash is doing. If you get the bride on her own then expect to ramp up the FEC. If you get the groom on his own then you might need to back it off. A good default is probably to nudge the FEC up a notch or two and then adjust from there.