When you're in manual, eveerything you need to set manually, thus you're adjusting your exposure.
When you change your exposure compensation, you exposure metering will change and you might not get the correct exposure reading when you try change the settings (e.g. shutter, aperture and iso).
When in other modes, you adjust the exposure compensation so that the camera will adjust the settings (shutter or aperture or iso) to get the correct exposure. So lets say you're in certain lighting, you took a shot, and you notice the exposure is not correct due to the area, you can change your metering modes, or you can adjust the exposure compensation depending on situation.
Lets say you're trying to take outdoor nightime, you want to capture those decoration spotlight, on default exposure, you most probably won't get the desired result, you will need to underexpose the picture so the background is dark, and the decoration spotlight lighted nicely as you wanted.
In manual mode, you simply adjust yourself all those settings (shutter, aperture, iso).
Nikon and Canon SLR VR/IS is on the lens, not body.
both type of VR have adv and disadv, on the lens, it benefits the viewfinder.