As far as I am aware, Munzees and geocaching are completely different games and are in competition with each other. I believe that geocaching.com won’t even allow the word Munzee on any of their cache listings. There even seemed to be a problem using the word on their forums.
As you correctly say Munzees use QR codes which are appearing on everything these days – almost everything you buy seems to have one on it. There should be no overlap as far as geocaching.com is concerned. Every geocache MUST have a cache (except earth caches, etc) and finding a QR code is NOT finding the cache and cannot be logged until you find the cache and sign the logbook.
The real confusion seems to be that many cache sites also have Munzees associated with them. You log the Munzee by scanning it but this is nothing to do with the cache. A good example of this is Log Ness Monster where there is a Munzee on the fence. Unfortunately Munzees often give away the cache hide.
