You can hide controllers by clicking Hide/Show when you have one or more Limber layers selected. Limber will then hide all the controllers from that set. If you have no Limber layers selected, it'll hide all the controllers in your comp. Alt-clicking the Hide/Show button will show controllers again in the same manner. Hiding and showing controllers turns their opacity to 0 or 100 rather than affecting the visibility switch for the layers, so that you can still see and edit the motion path when you select a hidden controller.
Start and end controllers change color when they are moved close to the limb's fully stretched out length, from green towards blue. When they reach the same distance as the limb's total length (and the limb becomes dead straight) they then change abruptly to red. This makes it easier to spot pops when you are animating. You can disable these color changes by shift-clicking the Hide/Show button. Shift-clicking again will turn them back on.
You can make controllers larger or smaller by clicking (or alt-clicking) the +/- Size button. This will re-size all the controllers from the selected limb set.
The automatic rotation of controllers, which you determine using the Rotate Start and Rotate End properties in the Limber effect, takes effect through an expression on their Rotation properties. This allows for you to parent your own layers to Limber's controllers, and have those layers stay aligned to the angles of the limb.
If you want to manually animate the rotation of your own hand and feet layers, you need to do this by keyframing their own rotation properties. You may need to adjust their anchor points in order to make them rotate around the right point.