The reason that you have multiple focus points lighting up is because the camera is in the "Auto" AF-Area mode. This is the factory default setting for AF-Area. See page 173 of the English D90 manual to learn more about AF-Area.
The Two-Button Reset does not reset the AF-Area mode. If you have the AF-Area mode of "Auto" selected, then the camera selects the focus point automatically, and there is no resetting of the selected focus point to center because there is no selected focus point.
Only in the AF-Area modes of Single Point, Dynamic, and 3D-Tracking does the focus point get reset to the center. You can then use the Multi-Selector to move the focus point (provided that your Focus Selector Lock isn't set to "L".)
The D90 manual has a great deal of good info in it. It's biggest problem is that the writing is information dense. That is, they compact lots of technical detail into few words. It's best to read the manual text slowly, reading and understanding each word before moving to the next. Just about everything you need to know is in the manual.