Look on Kayak http://www.kayak.com/flight or Matrix ITA: http://matrix.itasoftware.com/ for your flight options. Travelers from the US West Coast usually prefer to connect in Europe rather than the eastern US when there is no nonstop available (as in this case). There are two advantages: the overall flight time is shorter, and if your first flight is late, there will be many more options from (say) Frankfurt to Berlin than there will be from JFK to Berlin. You want your air travel to be all on one ticket; this way, if a delayed flight causes you to miss a connection, the airline is responsible for getting you to your destination. If you are on separate tickets, YOU are responsible, both logistically and financially.
Connecting in Munich is usually felt to be easier than connecting in Frankfurt, if you have a choice; both will have very frequent connections on to Berlin (not sure about Prague).
Yes, Rick has a Germany book, and a Snapshot Berlin guide that is directly excerpted from it (in other words, buy one or the other, but not both). You can investigate them on this website, here: http://travelstore.ricksteves.com/catalog/index.cfm?fuseaction=catalog&parent_id=159. And here's his Prague And The Czech Republic guide: http://travelstore.ricksteves.com/catalog/index.cfm?fuseaction=product&theParentId=157&id=290
These books have plenty of information about visiting on your own, and with his tips I found these cities very "user friendly." If you want a private guide, Rick lists some; I also like the idea of a walking tour, especially in Berlin, to start to grasp its history. Do beware the "free" tours offered in both cities; here's a blog post from Rick on the subject: http://blog.ricksteves.com/blog/the-ethics-of-aeoefreeae%C2%9D-tours/.