If using a binary install for 10.3 or 10.4 then it just renames your existing folder which should be at /usr/local/mysql<version> to <..._bak> and creates a new one for the 5.x install as well as making a symlink to the 5.x folder in /usr/local
It explains it all very well in the html manual, so get the current 5.0.18 version from the downloads page and read up first.
If some of your existing 4.x databases are having problems you can delete the symlink pointing to 5.x and recreate a new one to your old 4.x version. You should do dumps of your current databases from 4.x before you do the install, and then import them into 5.x once you have it all set up and running.
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