There is four ways to do so
Missionaries are quite cheap and if you can convert enough cities around the enemy they will eventually convert through passive religion spread.
You can just walk up with apostles and convert them, apostles are the troop designed to do just this job. There is a table in a thread called "finding my religion" that shows how many apostle charges it takes to convert it depending on the size of a city
You can defeat an enemy apostle/missionary/inquisitor near their cities which reduces their religion in the cities
You can conquer the city with military units, use a single inquisitor charge to remove the religion, use a missionary if need be to top up your religion there and then give it back
I tend to use a combination of all 4 in a game depending on circumstance at the time. I do tend to not promote my first few apostles or promote them if it's a weak promotion.... use all but one of their charges converting a city then use them for combat.
A strategy of using passive spread to your favour does work, it is important to convert non religious civs first as these do not complain about conversion and a group of their cities has a lot of passive power. Jerusalem is not to be underestimated in passive spread either, its quite strong.
Converting cities with missionaries that are not religious before the enemy makes the enemies job harder because missionaries are useless at converting a city that has a religion.
