In manual you control both the apperture and the shutter speed, if you change the shutter speed to a slower one you should see the exposure compnesation change.
What the exposure compensation reading is showing you is that the camera believes based on it's light meter reading that your picture is going to be underexposed which is why they are dark.
So the -2 you are seeing isn't actually exposure compensation.
Generaally I tend to use aperture priority or shutter priority depending on what I am doing, for example sports I would use shutter priority and portraits aperture priority, this mean I deal with the aperture or the shutter speed and the camera deals with the rest.
That is how I understand it, I am sure some one will correct me if I am wrong
