Sometimes the manual tells how to make a feature work but why you would want that feature is not so clear. The 550D actually has very few AF points, it is a weak feature. You should look through the viewfinder of a 1Dx! Anyway, you are correct, the middle AF point in a 550D and many other models is the only cross type AF point, and that makes it most powerful. Once you have selected a single AF point, that point will be the one that remains, even through a battery change, until you select a different point, or all points again. At least this is the case if you use Creative Modes: M, Av, Tv, and P. M, Av and P are the only modes I have ever used with that body, so I can't comment on what the green square and those others do. Since they set almost all options, they may affect AF points too.
When you have time to focus and recompose, the single centre AF point is a great option. Times when you can't use that point for one reason or another, the others are there to help out. Not everyone shoots only portraits or landscapes. Even shooting portraits, since you want at least one eye sharp, and you might be shooting with the lens open to f/1.2 or f/1.4, with a razor thin depth of field, recomposing may cause you to lean forward or back slightly. Just enough to throw off focus. Set the point where the eye is, focus and shoot. No recompose, quick operation between focus and shutter release, less chance of missing focus.
The manual says there are 3 focus modes. One Shot and Servo are the useful ones. One Shot for stationary and slow moving subjects, Servo for faster subjects moving toward or away from you. Servo tracks your subject, predicting where your subject will be an instant later. So, it is useful for shots like this one from Stanley Park's aquarium
https://www.flickr.com/photos/54048679@N07/9690241442/
But there is a catch. Since the camera is tracking your subject, you have to keep the focus point on your subject. That can be a challenge when your subject is fast! And you may not want your subject in the bull's eye. So, again the other points are useful. Turn them all on and your subject can be anywhere near the centre, instead of exactly at the centre. This helps a lot when trying to track your subject and it is moving around in the viewfinder. With practice you can get your subject on the point you want to use, and you can move the points around fairly quickly to use a single point if desired.
The benefits will become clearer once you start shooting.