From what I understand the Champions is part of the six bowl games selected to host semi's. Remember, it's a rotation. So, based on that, the Orange will get a semi-final, but it doesn't have any relation with a conference in that the four selected may not include one of the ACC teams.
If I understand this correctly, we'll have a season with two bowls hosting semi's. Let's say it's the Rose and Sugar. Then, you'll have traditional bowl games like the Orange which will select teams to play in their games. I imagine a bowl like the Orange will maintain their relationship with the conference they have a tie-in with during the years they aren't hosting a semi-final game.
You do bring up a good question of just how conferences and the bowl-tie in's we have now will look like in two years. It would make sense for it to remain close to what it is now. I can't see the Sugar not selecting a team from the SE, just like I can't see the Rose not grabbing their two traditional conferences.