Using pass

Hi travelling to japan in October with wife and 2 kids I think it will be worth getting jr pass we will be landing Tokyo then to Osaka then Hiroshima then Kyoto then Ramayana then Matsumoto then back to Tokyo. Am I right saying I will get value out of that. Do I order online then activate from station in Tokyo? Does it cover short trips in Tokyo or in Kyoto or Osaka? Do I need to reserve seats a day or so earlier or just show up at station?