Starting out in Manual modes

Sorry if you've mentioned which camera you use but for the Nikon's I own at least (D300s and D3s), using manual mode with auto-ISO is just like any other program-exposure mode. You use exposure compensation just like you would with aperture or shutter priority. Even though you are in "manual" mode, the camera is still deciding on the proper exposure (let's not get into "exposure" with digital and complicate this matter) so exposure compensation has the same effect you'd expect. Another thing that will be immediately obvious is that if your auto-ISO configuration has a minimum shutter speed setting that will be ignored in favor of your set shutter speed.