Once I add the Everyone account , it will override any other settings I have for other groups or users (if they inherit their permissions from the parent).  I recently allowed Everyone in a repository so that people could  download source code.  Then I made updates to the code today and went to check it in and found out I no longer had permissions!  Adding Everyone with Read Only access invalidated my committers group!

So the workaround is to change your other groups AFTER you add the Everyone account.