Accommodations that are easily booked in English tend to be modern, characterless hotels built for Japanese tour groups. Gorgeous lobbies and sterile, cookie-cutter rooms are the norm, although more attractive hotels are appearing as Japanese seek out lodging with more personality. Guesthouses or pensions are a cheaper and friendlier option, with welcoming owners who strive to impress guests with the catch of the day or wild vegetables on the dinner menu. Many (but not all) guesthouses have Western-style beds and regular sit-down toilets. Although booking in Japanese is the norm, simple emails via a website can work, too. Although you might not normally consider one, a youth hostel is also a decent alternative in Hokkaido, both for price and for the sense of spirit and camaraderie that you will not find in the more sterile hotels. However, some do not allow male-female couples to sleep in the same room. Hostels in towns and cities are usually clean and modern, and in the national parks, although in older buildings, they can be excellent touring bases.
Outside Sapporo and Hokkaido, most hot-spring hotels (onsen) charge on a per-person basis and include two meals, excluding service and tax, in their rates. If you don't want meals and wish to eat convenience-store food, you can often renegotiate the price (the word in Japanese is sudomari). Just remember that those hot-spring hotels and guesthouses are your best bet for dinner in remote areas. Also note that with Japan’s prolonged recession, some hotels may actually be cheaper than listed here. Some onsen offer combination rooms, a Western-style room with a tatami section where you could also sleep on futon. If you're interested in trying out a Japanese-style room but still want to sleep in a Western-style bed, this is the perfect option.
