JR Pass between cities, and within cities

Hello! I have purchased a Japan Rail Pass (Green) for an upcoming trip to Japan. I will be traveling to the following cities (in this order): Tokyo, Nagano, Kyoto, Hakone, Narita. I apologize in advance, I have a couple of different questions: I've downloaded Hyperdia but it appears I cannot reserve my seats through this app, and it appears that the JRPass does not cover all of the various lines to each city. 1) Is there another pass that I should purchase to cover to those transfers that JRPass does not cover, or do I have to purchase individual tickets on each travel day (I'm trying to avoid standing in line for tickets as much as possible). 2) Can I set up my reservations for all the trains at the time I go to the JRPass office to convert my voucher? 3) I only purchased a 7 day pass, so it will expire on my last day in Kyoto. Is there another type of pass I should get for travel from Kyoto to Hakone, and Hakone to Narita airport? I saw a Hakone "free pass" but I'm having a little difficulty figuring out whether it would cover any of those trains. 4) Lastly, if JRPass does not cover many trains within these 4 cities, is there another pass I should consider to supplement my JRPass? Again, my primary focus is to try and set up everything as much as possible before my trip so I do not spend a lot of time waiting in lines when there. Thank you in advance for any guidance you can provide!!