I think I am not doing this correctly...

I have a Nikon D90. When I use spot metering (and say I want to meter for two parts of a shot without altering the composition and the camera position - the highlights and darkest spot), how do I do It. What am aiming for (in terms of the focal points that I can see in the viewfinder)? Is it that when I change the focus points (Nikon has 11 points visible from the viewfinder) does it also use the same focus point for spot metering or is it something else that I need to use as my pointer to spot meter off a particular point? It also gets confusing as when I have auto focus on the camera automatically picks out a few points as it focus points - in that case how will I use spot metering (which is my pointer)?

Not sure if my question is clear but any help would be great...