Getting around within cities

Hello,

I am trying to determine if the 14 day pass is the best way to go. I will be in Japan for 11 days traveling from Osaka (4 days) to Kyoto (3 days) to Tokyo (4 days). It seems to be the best way to travel between cities but I’m concerned that I will have limited access within cities and will have to use a different line to get around, costing more money.

What is the best plan for this itinerary and how can I best get around within cities during my stay?

Thanks
Charles