Tocoo is usually the most expensive English booking site, and required pre-payment or at least CC authorization. Others such as tabirai are much cheaper, do not require credit card. I almost always book with rakuten (Japanese only), very often the cheapest.

If renting in Hokkaido, there are many English sites run by the rental agencies directly.

I have also booked on Toyota website (Japanese only). They do provide English phone booking and full customer support 7 days a week. I often called that phone line to arrange for hotel pick-up, or reserving Express Way passes, etc. It's toll-free inside Japan but otherwise a toll call, though it's cheap using skype etc.

I never prepaid car rentals in Japan.

Credit cards can be used to pay toll on Expressway, but toll roads within a city often do not accept credit.