Yes, there can be a trade-off between traffic volume, shoulder size, road condition, and (for me anyway) dogs. There's no magic formula or online route generator. Sometimes the small roads are safer than the big roads, sometimes not. Local knowledge can really help - stop and ask people who live in the area.

For higher-level planning, visit AdventureCycling.org for cross country and other long distance pre-planned bike routes, as well as guided tours and learn-to-tour classes. You can buy route maps from them, and I think this is a great thing to do for your first tour, they have lots of info on where to stay, services, elevation profiles, distances, so you can focus on the enjoying your ride without being too stressed out about routing. They do a pretty good job picking safer/nicer roads - but sometimes make mistakes too.

visit crazyguyonabike.com for on line bike touring journals, you can look at where other folks have ridden.

many state departments of transportation have information about roads that may include traffic volume and shoulder information.

talk to local bike shops and bike clubs about the riding around your home town, they might have some routes posted. Also good to do on tour, if you are trying to route through a city, you can ask the locals (phone, email, stop in).

there are a bunch of online mapping sites that people upload their rides to, i find them not very useful, but you can google around - mapmyride, routeslip for example.

RE: churches - I haven't done that, but I have stayed at city/county parks and fairgrounds. You just have to figure out who to ask - try police, library, fire dept, chamber of commerce. And watch out for the sprinklers. look at the "stealth camping" threads here and on crazyguy for info about different ways people camp. Personally I like to camp on BLM/forest service land (always allowed) or established, legal campgrounds. Not "steal"th. But that's just me.

Welcome to touring!