How to book a ticket if my pass covers only a portion of my trip?

I'm thinking of buying a regional pass (Sanyo San'in Northern Kyushu pass). One of my trips will be from Hakata to Tokyo. I believe this regional pass covers only the Hakata to Kyoto part. How do I book a ticket for this trip? Can I book one ticket for Hakata to Tokyo and pay the difference for the portion not covered by the pass? Or do I have to book two separate tickets - one for Hakata to Kyoto (included with the pass) and one for Kyoto to Tokyo (pay for this separately)?