I use symlinking from a master copy, this has bit me in the ass enough that I now keep a full copy of WoW and copies of all patches. I also download my patches from fileplanet rather than depend on the blizz downloader (it's faster for me, and doesn't muck with the registry)
I don't know if this will help anyone, but for Mubox users I wrote up a howto for those who get bit in the ass like this, from my own experience: http://mubox.codeplex.com/wikipage?t...ly%20a%20Patch
Two write-ups, one is how to apply a patch, the other is how to fix a bad patch. Some of the subject matter is specific to Mubox (e.g. Game Isolation) which is why this is even a problem (multiple copies, or run locations), but it's otherwise the same regardless of toolset.
Hope this helps, if not do share your experience, we can all benefit.
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