Joban/Chiyoda line question.

Hi there, me and a freind are going on a trip to Japan later this month. We both have JR rail passes, and we are staying near kita matsudo station which is on the Joban line. However it seems as if the Joban line changes to chiyoda metro after Ayase station. How does this work in regards to fares. If we get on at Kita Matsudo can we use our JR passes all the way through? Would we need to get off at Ayase station and pay a seprate fare? It would be great if someone could clear this up, thanks.