At the risk of sounding like a tape loop, there are entire guidebooks devoted to both Tokyo and the Kyoto/Osaka area.

You have plenty of time to read up on both regions, so start reading, and then come back with specific questions.

But yes, I think that starting in Tokyo is the obvious choice. Even if you have to do a roundtrip on the train (which would make a JR Pass worthwhile), train travel is much less hassle than plane travel.