I guess you just span missionaries as long as you can get the instant yields somewhere? What do you use the resources for usually? (to do you rush some wonders? build up military? infastructure?)
The idea with both, for me at least, is to spend 100% on Missionaries until there are no more cities you can reach that are empty of religion (after that I usually enhance, getting buildings as a 2nd belief, and then build them all before maybe another conversion push.) Apostolic I usually use with Tradition, because the capital is very needy of population and this can make it large very quickly even without very food heavy land (though I sometimes also use it with Progress or Authority if the capital's land is just A+ amazing.) The culture you get is pretty extreme too for the earlygame, it's like 200+c from a 200 faith missionary with decent spread targets. Basically it lets you vector your faith generation into culture while getting side benefits of spread religion and lots of food. Later in the game even a Great Prophet can be kind of like a Great Writer, getting massive amounts of culture from doing 4 spreads to big AI cities.
Also, Apolistic can turn into the ultimate in jerk spreading religions, since you're happy to fight over the same city again and again turning your Faith into Culture and Food each time, rather than losing it entirely. It's kind of like the Authority of Religious conflict. One particular jerk move is to have a GP ready for when you make peace with an AI of another religion, and then send him in during the treaty to convert four of their cities and make a thousand+ culture/food total. Or if you really want to get into a religious grudge match with the AI, build Bourbadour and also take the Enhancer that lets your missionaries erode pressure.
Council of Elders is probably more powerful, but unlike Apostolic's lazy micro (Food and Culture basically don't need micro at all) you need to micro CoE very well to get the most out of it, aiming your techs correctly and dropping hammers at the right moments for needed Wonder timings, and you also can still sometimes lose a Wonder to random stupidity. Council of Elders also has an advantage though that if you convert 50%+ of a neutral civ's cities, they may start to spread it on their own and give you huge buckets of hammers and science at random times. Unlike Apostolic it has less of a future, since it doesn't scale with followers converted, AND you can't repeat cities, so Great Prophets can't give you huge buckets of neverending rewards, and you don't get rewarded for endlessly contesting the same cities.
That being said though, Council of Elders is totally bonkers in Medieval when you combo it right and use it for wonders or timed new unit pushes (through for example a Heroic Epic capital where you slam the hammers into units.) Isabella in particular is a serious offender, being able to trigger it with both missionaries and settlers and city captures.