Exactly, casas rurales are entire country houses, but some can only be rented in their entirety and some have rooms that you can rent, of course if you're travelling with a group big enough to take up all the rooms available that's a possibility too. In the first case while you're staying in the place you're pretty much left on your own, though both meals and/or laundry service might be available; and in the second option the owners or whomever runs the place are likely to be there fulltime, and that's as close as you can get to a bed and breakfast, really. Other variations are posadas rurales, hoteles rurales, hostales rurales, etc…. And as Mman said, B & B don't exist here, so if you just showed up in some village you would have to ask the locals if there is a hotel, hostal, posada, casa rural, or any rental apartments around where you could stay.
Personally I adore these places, but most of them, in fact, many of the most interesting ones, which are so attractive, among other things, for their out of the way location, cannot be reached by public transportation (and by that I'm not including taxis, but that would be quite an expensive option). So my advice is that either you choose to go to a very interesting town with plenty to see, or do (trekking, horse riding, and other outdoorsy activities), or don't stay in those if your plan is to be travelling back and forth to Madrid and some other bigger places, because that could be a pain. Also, the most worthy ones don't necessarily have to be on the cheap side, since the décor, surroundings, activities, and service can be top class; maybe the cheapest option within this category are hostales and posadas rurales.
Do check out the recent thread Sierra de Gredos region; by that I'm not implying you should limit your research to that area at all, there are plenty other areas just as nice around your own “places of interest”: Andalucia, Galicia, etc…, but there's info there that can give you a general idea about this type of lodging, webpages, etc….I posted the sites for several very pleasant places at the bottom of it, and also, as always, I recommend www.secretplaces.com
, it's English version, will probably help clarify things for you.