Haneda Hakone

Hi, I plan to visit Hakone and spend 1-2 nights.

When I arrive at Haneda international airport, I plan to travel directly to Hakone.
I will choose a hotel ryokan that is near to Hakone Yumoto station so that I can check in and drop luggage. I really don't want to bring luggage around with me and I hope I still have some time to spend at Yunessun after check-in hotel.

Then on second day, I would like to do Hakone round course.

May I know what is the best way from Haneda airport to Hakone?
I understand it is direct bus but I will be getting Hakone Free Pass.

Thanks in advance for your advice! :)

You can purchase that pass at Odawara stn.
http://www.odakyu.jp/english/deels/freepass/hakone/

Change dep date and time at page bottom.
http://www.hyperdia.com/en/cgi/en/search.html?dep_node=HANEDA%20AIRPOR...

By limo bus for Yokohama stn is no transit,
but it is easier transfering at Yokohama stn and cheaper is Keikyu(trains).
And, don't forget to read limo bus baggage limit note if will,
Rail company's baggage limit is not so tight, it will not be a problem mostly.
https://www.jreast.co.jp/kippu/20.html
http://www.keikyu.co.jp/file.jsp?assets/pdf/train-info/tetsudoueigyou/...
(use Google translate)

After Yokohama, you can also take JR's LtdExp train "Odoriko" or "Super View Odoriko",
http://www.jreast.co.jp/e/routemaps/superviewodoriko.html?src=gnavi
https://en.wikipedia.org/wiki/Odoriko
but there is no bus in this section,
rapid(until Kozu) or local(stopping all stns) of regular commuter train(s) are enough.