Selecting what train line to use.

I been using two Japan train apps to check how to get from location to location, example Hiroshima to Kanazawa, the app JapanTravel suggests Nozomi then Thunderbird then Tsurugi, my understanding for the Nozomi section I need to pay more I do not know how much more. The JapanTransit app suggests Shinkansen then JR Hokuriku line not sure if both are covered by the JR pass.
Is there some app where it is clear how I can travel on my holiday making the best out of the jr pass.
It is difficult when app suggest different lines and I do not know if they are covered by the jr pass.
Look forward to your reply.