Jamie,
I'm sure of your work flow, but you should be able to do the following:
1) You have music on the iPod. This came from a previous sync. The sync is based on your sync options - e.g. playlists, smartlists, etc.
2) You change the tags in your music library using MC. These tags are for music that is stored on the PC.
3) You resync the iPod. The iPod should be updated for the tracks that changed as a result of the tag changes.
4) You eject the iPod and you should see the changes on the iPod.
If you are manually syncing the iPod (drag & drop), the tag changes you make will not automatically be resynced. You can of course drag and drop again.
MC 12 handles this situation very well. I do it all the time. However, the sync, to the best of my knowledge, is not checking each and every tag to determine if the file on the PC has to be resynced to the iPod. It is actually comparing the date of the file on the PC to the date of the file on the iPod. So a lot has to do with what tags you are dealing with and if those tags are being stored in the files. As an example, I have my cover art embedded in my MP3 files (Store Images In Tags Also). When I update my cover art, it updates the file and it gets picked up next time I do a sync. If I was not embedding the cover art in the file, MC may not be resyncing that file as it did not detect a change.
Assuming you are using the sync options to sync based on playlists or smartlists there is a simple way to determine what is going on. If you sync your iPod, it will show as fully synced in the Sync Handheld action window. Now go to the Audio button and select something in your MC library to do a tag change on. After you change the tag, go back to the Sync Handheld action window and it should now show one file that has to be resynced. If you click on details (right under the sync button), you should see the file you changed.
Hopefully this helps.
Randy