A few weeks ago we wrote about the reputation changes introduced by patch 5.2. Consider this small article to be just an addition to the old one.

A few PTR builds were added and now we know exactly how the championing will work in patch 5.2.
Here is how the UI was changed to help you with the new style of championing:

As you can see the reputations tab has some little stars there. Those are just some check boxes and if you are checking one then that's the faction you'll be rewarded reputation with while finishing a dungeon or scenario.
You can select only one faction at a time and the final reputation reward is going to be affected by all your reputation bonuses. If you are using the Commendation for a faction then your rewarded reputation is going to be doubled. As you can see, the factions that you purchased the Commendation for, have a little arrow added to their reputation bars.

You'll get 750 reputation for your daily dungeon and 325 reputation for your daily scenario.

Unfortunately you can only select MoP factions, with a few exceptions of course. The old factions reputation has to be earned the old fashion way. But that's why we have a handy Reputation Calculator to help you out