What are you trying to take photos of and with which lens.
1. With manual (non A type) lenses, only M mode will work.
2. To Use it, set your aperture ring to the desired opening and hit the green button (On top next to the top lcd).
3. If you're happy with the shutter speed the camera selects, take your photo.
if you are using an A type lens, set it to A and you can use one of the other modes, Av or Tv. In which case, use your e-dials to change the aperture or shutter speed (you can also do this in M mode where you can control both at the same time). If you are using Green Mode, Don't.
Also, make sure you are running proper firmware (press and hold the menu button while turning on the camera). You want it to be at least v1.20. It turns on a lot of features not shipped with the original camera at v1.00.
To really be of further help though, we need more information.