Itinerary with the JR PASS

Hey there!

We just purchased the JR pass for 7 days and we are now organizing our trip, I thought you might give us a little help :)

We are staying 7 days in Tokyo. Afterwards, 5 days in Osaka, and we were thinking to take day trips with the JR Pass to Kyoto, Hiroshima, Nara and Hakone from Osaka. I start to check the shinkansen timetable with hyperdia, and so I was wondering if during our JR PASS 7 days, we could take the trains as much as we wanted, with no limit ( since we would like to do day trip) ? which station is the easiest Osaka or Shin-Osaka to take the trains ?

The timetables in Hyperdia are showing many trains such as LTD. EXP HARUKA 9, JR Yamatoji Line Regional Rapid Service for NARA, or Hikari and Sakura for Hiroshima. Or can i know which trains I can and cannot ?

Also if we reserve seat, do we need to pay extra ?

Thank you so much for your help, very much appreciated !! :D