its knockout and the winners and 2nd place of the first groupls play pre determined winners and 2nd place teams from other groups.
Once it gets to the second stage (after the leagues) its like on 2 seperate halfs (i am sure you can imagine the 1/2, semi final, final equation)
So for some teams it is just impossible to meet in the final. For example we play brazil in the 1/4's. It could never have been a brazil x england final as both teams if they did the best they could do (they did) would meet here so one would be knocked out.