To expand on casperwb's comment above:
1) To change the number of focus points, press and hold the AF mode button (left side of the body), then rotate the sub-command dial (FRONT of the camera). You can verify the change by looking at the top LCD.
2) In AF-S mode, you can only change the number of points between one and AUTO. You need to be in AF-A or AF-C mode to have the full AF area selection (single, dynamic 9, d21, d31 and 3D). To change the focus mode, press and hold the AF mode button then rotate the main-command dial (REAR of the camera).
3) When manually moving the center focus point, the viewfinder will only show ONE of the selected focus points (i.e., the center point). Be sure to disable to 'focus selector lock' select the center focus point.
4) You can press the INFO button to see the positions of ALL of the focus points on the rear LCD, not just the center point shown in the viewfinder.
5) The menu item a6 ("Number of focus points") can be used to limit the number of selectable CENTER point positions, from 39 positions to 11 positions. I.e., when set to AF11, the multi-selector dial can be used to place the center point to only one of 11 positions instead of 39. This setting can be useful to quickly move the center point from one side of the frame to another. On the flip side, if you want to be able to fine-tune your CENTER point position, select AF39 instead.
6) This a6 setting does not limit the number of focus points actually used by the AF (which is determined by bullet #1 above). E.g., you can set AF11 to quickly select one of the 11 center points, with the AF area set to 21-point dynamic focusing.