Help? Options

[cheela]

So I'm gonna be going to Japan in like two weeks and this is my second time there.
I'm going through a program and they're paying for our plane ticket and providing us with some food n shelter
and whatnot but for two weeks we'll be on our own. Me and my girlfriend are trying to budget ourselves
so do you guys know any cheap places to stay in? We're gonna be around Tokyo and Nagasaki but, we also have
a JR Pass so we can travel around too. So, any of you guys who have been to japan or are still there now please give me advice! thanks.

PS. I know that youth hostels are probably the cheapest it can get but, can you share a single room? cuz I looked online and
they only let you pay per person. so it doesn't matter if you rent a single room or a double room. just wondering. thanks