When the camera is in manual mode, it does exactly what you tell it. It opens the shutter and stops down the aperture according to what you set. The E-TTL flash system will account for any ambient contribution and attempt to properly expose the shot as long as it has enough power. If your combination of distance, aperture and ISO require more power than the flash has, the shot will be underexposed and you'll need to adjust accordingly.
ChrisBlaze wrote in post #2688423
The only reason I used the Sto-Fen was because I was told that using the flash without a diffuser causes a harsh look.
This just proves you can't believe everything you hear.
If your shots look "harsh" (and that's a somewhat vague term that means different things to different people), it's usually not the flash unit's fault, and it's not necessarily something a plastic diffuser can solve. If those things magically improved every shot, they would be standard equipment on flash units.
The Sto-Fen can be useful when you have low-white ceilings or other suitable surfaces to bounce some light off, but they also waste a lot of light and reduce the flash unit's effective range. Such devices need to be used with care.