Found a good reason to check the checkbox I mentioned earlier: when your origin and/or destination are different from the trip for which you want a reservation.

Shinagawa jr rapid train to Tokyo Shinkansen to Koriyama to jr rapid to Aizu Wakamatsu. But the only part you can book online is the Shinkansen.

You check the box for supplement and reserved seat ticket only. When you go to pick that up you buy the base fare ticket from Metro Tokyo Area (includes Shinagawa) to Aizu
Otherwise you have to get three tickets one for each leg of the trip
sorry if not clear

A lot of great information here mrwunrfl, a lot to take in. I appreciate your help. I will for sure buying tickets as soon as they come available. As for day trips, eg tokyo to fuji, tokyo to kamakura - do these also need to be booked in advance over this period?

There is a Fuji Excursion train from Shinjuku that only makes two round trips daily. There are reserved seats and supposedly unreserved seats if the reserved don't sell out. I bought mine in advance last year to ensure I had a seat....

Pretty sure it would be regular train to Kamakura.
Something like Yamanote Line to Shinagawa then rapid train to Ofuna and then the Enoden train iirc
Mara gave info for Kawaguchiko but maybe you mean Hakone