You can only set a single point manually on the 50D.
The way that auto point selection works is that when presented with the scene to be focused on the camera will evaluate all of the available focus points. Given that info, it will "decide" where the subject is (usually by focusing on whatever is closest to the camera, although if there's light at the top and dark at the bottom it will usually understand that the bottom point is foreground). If several AF points cover things at the same focus distance, it will display that more than one point is at the same distance by lighting up all relevant AF frames.
So, there is a difference in the way the AF frame display is used between manual and auto - manual the AF point highlight shows which frame you have selected while auto it shows which are in the plane of focus that the camera thinks is correct for the scene.
Note that there are other bodies where things are a bit different, with hidden "assist" points (EOS 5D and 5D2) and AF area expansions (where multiple adjacent points are used as one big point - EOS 7D, 1D series, 1v, 3).