Hi rhraziel and welcome to the Q&A Board!
If I am an manual mode and I have all my exposure settings dailed in, does the metering change those settings to get a better exposure?
No, the metering system won't select better exposure settings when using manual mode. However, the in-camera indicators or watching changes on the LCD should give you a pretty accurate indication of when you've properly exposed a shot.
Also, When I'm using "Spot Metering" I can't move the "Spot" (Or at least not that I can tell). So the subject always has to be in the center of the frame. This doesn't work well you're trying to take a picture using the rule of thirds. Am I missing something?
Some cameras let you move the single area focus indicator from the center, though I'm not sure if yours does so check the manual. However, the subject doesn't have to be in the center of the frame to use the spot meter appropriately.
After selecting Spot Meter mode, position the spot indicator on the area you wish to meter. Depress the shutter-button halfway down to lock exposure and focus, then recompose. Once you have the desired composition, depress the shutter button all the way down.
This two-step process is one of the fundamental techniques in digital photography. The following example doesn't deal with spot metering, per se, but illustrates how to use this important technique:
http://www.digicamhelp.com/focus-exposure-lock/index.htmLet us know if you have further questions.