Hi LotsofJazz,
To disable MCE in vista:
How to Disable (Uninstall and Remove) Windows Media Center in Vista My Digital Life
I used this codec guide:
MEDIAPORTAL - free MediaCenter HTPC Software - simple mediaportal codec guide
I use CoreAVC for x264 HD stuff, and Dscaler for Mpeg stuff. To be quite honest I never even bothered to set merits or check if Windows uses the codecs I want, because I simply use MP for this. In MP you set for each media type which codec it should use.
Hope this helps.