In Tokyo I only stayed in a hotel once, it was actually outside of Tokyo, a Hilton adjacent to Disneyland and it was around $400 US a night for a family of 5, but it seems like a lot of that was a per person fee so if it is just a couple it would be much cheaper. As for how you pay we just put it on our American Visa card and it was just the same process as any good hotel in the US.