Maybe it's just the sessions that I've been involved in, but it doesn't seem very often that religious characters go out of their way to evangelise their belief to others. I've seen it in a few games, usually on the part of a player who just wants to get in a bit of roleplaying through exposition with NPCs. Religion is just a surface coating on a character, maybe it provides certain spheres (or domains) of clerical magic, or restricts access to certain weapons, but it's rarely a functioning belief system.
The prayers of these characters are simply another form of magic, sometimes they even use the same spells as traditional hermetic magic users or instinctive sorcerers, but they acquire them in different ways (according to their domains or spheres, rather than through schools or mentors).
I'd like to develop a system that relies on belief, something that will apply to mages (who use their own belief to fuel their mystical effects) and religious types (who rely on the beliefs of those around them to empower their effects). Let's give some name to the two opposing classes of mystical characters; there are mages who weave magic, and there are clerics who channel miracles.
Put simply, a mage will often work alone and may actively avoid religious types who are inclined to use their beliefs as a form of countermagic. Religious types need to spread the word of their faith to make it easier to work their miracles, they may seek to wage war on other faiths to reduce the power of opposing miracles. Theurgists would gain the power of their own faith and augment it with the beliefs of those around them, working miracles empowered by their own energies and the energies around them.
Places of power might exist (which is pretty common in most fantasy settings), such places of power may be claimed by a mage (especially in the wilderness, or on lost islands), or may be the location of a temple and through the congregation of followers their power might be channelled to a cleric. Some places of power might remain hidden, simply seeping their energies to the outside world around them until someone claims them (perhaps a hidden glen, grove of sacred trees or spring of water).
Such places naturally become the focal points for adventures and eventually towns are built around them because people feel the energies at an instinctive level. Factions would work to claim such locations, but it takes numbers of people, regular rituals and consensual belief to anchor their power.
If places become significant in the game, then that leads us back to one of the favourite topics of this blog...maps.