I originally posted about how I needed XBMC to have a shared backed. While this would be ideal, I think I have found a "workflow" that will work for me.
Initially, I thought that the XBMC database would be located on my main machine and it would be referenced using mklink from the PC hooked to the TV. This was because I assumed that I would be watching videos from my main PC using the XBMC interface. Now I realize that this does not have to be the case.
I modified the AdvancedSettings in XBMC, setting the "cleanonupdate" property to true. This will remove Library entries when performing an update when the files do not exist. This is perfect for me because I can keep watching videos from my main machine and just delete them when I am finished (which is what I do now) and XBMC will reflect this change at the next update.
Now I just need to get the libraries set up to back up to my NAS in a sensible way.