how to use ethnic (religious) cleansing
how to use a missionary:
1) the colony/city you want to convert must be less than 5,000 population
2) send a normal colonist (settler) into that colony/city
3) once the colonization attempt has been successful, that province will be converted to your current state religion.
Simple process.
You ask, what if the city I am trying to convert already has a population over 5,000? What then?
Answer: there is a tactic to deal with that called 'ethnic cleansing'. Actually, it's religious cleansing, but it accomplishes the same thing.
For example:
You captured the small Catholic province of Ulster, but you want to convert it to Protestantism (let's say it's your state religion)
So you then place your relgious tolerance slider against Catholics to zero (the far left).
This then will make your single Catholic province upset and more likely to rebel against you. That's what you want to happen. You are exactly trying to provoke them.
When the rebellion happens, let them rebel until the rebels TAKE your province. This process will kill off some of the population. Sometimes it's enough to lower the population down to 5000 or less.
Also when you send a seige army to recapture that province, after the seige is successful and you recapture your province, the province population will decrease even some more!
Repeat the process as necessary. Once the population is below 5,000, you can send in the colonist (missionary) to "convert" the heathens.
Voila. You now have a province that is loyal to your state religion.
By the way, I am not related to Slobodan Milosevic in any way, shape or form.