Can I clarify some things re my Hakone trip?

I will be traveling from Shinjuku to Hakone and stay in Hakone for 4 nights and 5 days. I would like to clarify and verify the following:
1. The Odakyu Romancecar train to Hakone-Yumoto costs 2,080 yen for a one way trip only? If so, do I purchase a return ticket also in Shinjuku or buy it in Hakone for the trip back?
2. The Hakone Free Pass good for 3 days is 5,640 yen and does not include the train ride from Shinjuku to Hakone? Does the Odakyu train ride from Shinjuku to Hakone already count as Day 1 for the Hakone Pass? I am asking this because I will most likely arrive in Hakone by late afternoon. Therefore, I can only use my pass for 2 whole days of my 5 day stay?
So are these 2 separate things I have to pay for? Or is a one way Romancecar train ride included already if I purchase the Hakone 3 day pass? I got confused when I read a suggestion to consider a Hakone 3-day pass which includes the train journey from Shinjuku station via Odawara and other local bus and train rides.
From...Jay

http://www.odakyu.jp/english/deels/freepass/hakone/

explained in their website.

romance car is not covered by any form of pass. you can pay extra to ride the romance car.

yes the 5650 yen version is for 3 days. if you dont want a pass to start on the first of your five days. you just pay the full fair for the train ride, and by the "from Odawara" 4500 yen version from odawara on the second day.

Thanks a lot!