Hi there!
The Akasaka Excel hotel Tokyu is opposite the Akasakamitsuke metro stop, so it would be pretty convenient I think. Of course, if you think you will be tired, the limo bus is a good option.
The 2 day metro passes do have to be used on consecutive days. There is also a 1 day pass which you may find more convenient (though this is more expensive comparatively).
If you do have a local friend who speaks Japanese then yes, they can make seat reservations for you, however they will have to pay the small seat reservation charge (free seat reservations are only available on presentation of the JR Pass). When you arrive at the station, you should be able to refund this reservation charge and re-reserve using your JR Pass, however there will be a small window in between reservation refund and re-reserving where your seat may be taken. On balance, if you think you'll be travelling on an extremely busy day (Eg, new years day), then it is well worth it, however outside of the 31-2nd period I think you'll be fine to make your reservations on arrival in Japan (unless you are on a tight time schedule).
Reserving seats reserves a specific seat on the train within reserved seating cars.
Both types of JR Pass, "Green" and "Standard", allow for free seat reservations. The Green class (or first class) is all reserved seating, however standard class has reserved seating cars and non-reserved seating cars. In the non-reserved seating cars you can simply turn up and get on the train, however reserved seating cars will all require a reservation (which can be done just before you board in most cases). Green class tends to be much less busy, however for most use the standard class bullet train is very comfortable.
Hope this helps!