All right. You want to come to Japan. You want to travel off the beaten path, away from Fujisan (富士山), Kyoto (京当), and Tokyo (東京). Many have tried, many have succumbed to the foreigner-friendly suggestions from Lonely Planet and Frommer's.
Where do you want to sleep? A minshuku (民宿) in rural Kyushu? A hot springs ryokan (旅館) near Aomori? (Incidentally, there's not much difference; ryokan tend to be more expensive and offer private dining; minshuku usually have you eat as a group with the mama-san. Both are Japanese style. The quality of either depends on the area.)
I know you're looking to be comfortable as you travel, and it's very tempting to stick with clear English directions, English suggestions, and lodging areas that have proven themselves to be open to international guests.
There's nothing wrong with them, per se... but you can definitely see the effects of tourism wearing down these once traditional houses, and taking you further from Japanese culture than you might have envisioned when making the reservation.
With that in mind, I suggest two simple, straightforward ways to find lodging in lesser-known parts of Nippon:
1. The best, by far, would be to just play things by ear and look for a place when you arrive. Naturally, this may not be possible (or convenient for those who don't speak Japanese). Try to avoid asking the tourist information center, if the area has one. A good idea would be to find a seasoned local or a police box and ask for their recommendations:
近くに安い民宿はありませんか？ Chikaku ni yasui minshuku wa arimasen ka? Is there a cheap minshuku in the area?
Again, depending on your Japanese level and familiarity with the country, sometimes an インターネトの予約 is just easier. Keep in mind that if the area has a member of the Japanese Guest Houses or a youth hostel, you'll most likely be directed there; keep a guidebook on hand to eliminate those choices.
2. On the internet. I know this may seem like common sense, but I'm sure plenty of people overlook it. Google your search in Japanese, not English. This will ensure you reach the main website of the town you will be sleeping in, and possibly a few local lodging websites.
10th hit on Google gives me a site with every single place offering lodging on the Mishima island chain.