You won't need advance reservations before arriving in Japan but Green Car seats are all reserved so you will need to reserve them before travel.

I'd suggest making your seat reservations at the same time you activate the exchange order and receive your actual Rail Passes. The best time to do that is immediately upon arrival in Japan, at the Japan Rail Service Center at Narita Airport - or Haneda if that is where you will arrive. You can also reserve seats for any deluxe express or limited express trains at the same time or at each station you arrive at while moving around the country. October is the start of fall color season so trains are still pretty full for those trains you can access with a Rail Pass. Remember that you must purchase the Rail Pass exchange order before you arrive in Japan. Most of us use on-line or phone order services from authorized travel agents.

Local line trains have no seat reservations so you can't do that anyway. Just walk on your desired train, showing your Rail Pass.

It is pretty easy to figure out potential trains and have a written list before you leave using HyperDia. Most JR agents speak English but they appreciate it when you have your needs written out as it is easier to understand. They are pretty helpful about fulfilling requests for seats together, aisle or window seats, etc.

http://www.hyperdia.com/en/ . Remember to use the "Search Details" screen and uncheck "Nozomi/Mizuho/Hayabusa" as those trains are not available to Rail Pass users.

EDIT: I just noticed that you are a UA 1K in the SF Bay Area. That suggests the possibility you might choose to arrive in Japan via Kansai International (KIX), which is outside Osaka and relatively close to Kyoto, rather than Tokyo. That is actually my preferred access route to Japan via SFO. If you choose to do that, it is even easier to exchange the Rail Pass and make seat reservations at the KIX rail center, on the second floor of the Arrivals Hall and across the street by way of the elevated walkway. Either way, NRT, HND or KIX, you can take care of all the Rail Pass and rail seat reservations in one place, immediately after arrival.