Uummm, actually DH_Epic, I already had a model for Conversion and Schisms which I put forward EONS ago (or at least it feels that way!)
Basically, the 'flat' chance of conversion is based on your nations 'religious culture', which is generated by religious improvements and 'cleric' specialists in your city. It can be significantly boosted, BTW, if you have and use a 'Religious Great Leader'. Like normal culture, 'religious culture' will flow across relatively open borders and into foreign cities close to said border. As the culture builds up in a city, there is a chance, per turn, of it converting a set number of citizens to your faith. Of course, there is also a chance of that happening to you too! In addition to the slow, natural conversion, you also have chance to 'evangalize' a specific city-using your nations resources. The chance of this succeeding is higher than normal conversion, and is enhanced even more if you have previously established a 'cultural enclave' in the city you target.
Anyway, this FLAT chance of conversion is modified by a number of other factors. There is the natural resistance of the faith to which the target civ belongs. There is the relative 'conversion strength' of the religion to which you belong (Monotheistic Faiths are better at conversion than Non-Deists, which are better at conversion than polyethiestic faiths). Also, the degree of 'Nationalism', 'Spiritualism' and 'Libertarianism' of your society, the relationship between your two culture groups, and where your religion sits on the other civs spectrum of 'most preferred' and 'most shunned' religions!
Now, Religious schisms can occur when a significant proportion of a city's population is of a different religion to that held by the State. Clearly, a State with NO official religion is not going to suffer from Schisms (but will also not benefit as much from religious improvements, or be able to make any 'cleric' specialists!) Anyway, depending on how 'Spiritual' and 'Authoritarian' your civ is, as well as how corrupt and/or unhappy the city currently is, there is a chance of a 'religious schism'-which essentially amounts to a religious 'civil war'. It first begins with said city (or cities) going into outright revolt, demanding a change in the State religion. If this does not occur, or if you don't do something else to change things (like reducing spiritualism or increasing libertarianism) then the city will break away from your empire. Like a normal civil war, this could mean the formation of a new nation, with a state religion in line with that to which the dissenters belonged!
Now, please note that this can refer to different 'brands' of a religion, as much as it can relate to altogether different religions. For instance, Eastern European polytheism is different from its Western European counterpart. So you might have a Western European city converting to 'Monotheism (East European)'.
OK, now a few things I failed to mention before:
Your religion type will also influence how effective luxuries are in your civ. Non-Deists are the LEAST effected by increasing amounts of luxuries(both in the positive and negative sense)-as they focus predominantly on the well-being of the mind rather than the body, and seek a fairly non-materialistic path for its followers. Monotheistic faiths are next in this progression, as they do tend to focus peoples minds on 'The next Life', rather on the benefits or detriments of 'the here on now'. Polytheistic faiths are the most effected by luxuries, as they encourage their followers to enjoy this life, rather than worry overmuch about the next one.
Aside from your main 'religion type'. You could also be able to set your peoples 'sect'. The main ones I can think of now are: 'Blood Cult', 'Orthodox' and 'Reformist'. 'Blood cult' makes you less susceptible to conversion and schism, grants you access to sacrificial altars as means of increasing happiness and increasing religious culture, but is only open to civs with high 'Militarism' and low 'Libertarianism', and is also very susceptible to corruption. 'Orthodox' is also fairly resistant to conversion, but is more open to schism. It allows for improvements that can change converts back to the 'proper' faith, but is also prone to corruption. It also requires a high level of 'Spiritualism'. Lastly, 'Reformist' is more susceptible to conversions, but is more resistant to schisms. It has lower base corruption than the other two sects, but their religious buildings produce less culture, and this sect is only open to civs with a lower than average 'Spiritualism' level.
Anyway, thats how I would like it to work, pretty much

!
Yours,
Aussie_Lurker.