Advanced Religions is going to be really cool. Advanced religions introduces city religious makeups to the mix. In BtS, a religion is either present in a city or not. There's no more to say. With advanced religions, however, each religion has a percentage of the city that is faithful to it. There is also religion loyalty, which affects how well people will be converted to a new religion. This is affected by religious buildings and civics.
The happiness produced by a religion will depend on how many followers it has. For example, if the state religion has 10% support, it will generate a lot less happiness that if it had 75% support.
There will be a bar showing the various religious factions right above the civilization culture bar in the city screen.
Missionaries will be able to get promotions from promoted monasteries (Via Asaf's Power Up mod. Thanks!). These promotions will increase a missionary's effefctiveness in spreading religion.