Just to add - Hakone Free Pass comes in two different types. One that you can buy from Shinjuku in Tokyo, which includes the return Odakyu Railway trip between Shinjuku - Hakone Yumoto, in addition to different means of transportation "within" Hakone area.
The other one is the type you buy at Odawara or Mishima (or a few other major stations) at a reduced price compared to the above, and does NOT include the Shinjuku - Hakone Yumoto trip. So this one is just for transportation "within" Hakone area.
As you have a JR pass, you already have the pass that covers the trip from Tokyo - Odawara on JR train. So you can use the JR pass to get to Odawara, then buy the Hakone Free Pass at 3,900 yen to ride cablecar, "tozan" (mountain-climbin) railway, etc. within the Hakone area to do the "round course." ENjoy!