If you're only staying 2 weeks as you say, you'll have to make a decision about what you want to see. If you absolutely insist on Prague, then do a Bavaria/Prague tour, going through southern Germany, Munich, and Prague. That's plenty. You could take trains--that'd be easier than trying to drive.

What *I* would recommend is getting a German Railpass and sticking to Germany. They're good for varying amounts of travel within a month long period. I did a 2-week Germany tour some years back with a five-day railpass. Flew into Duesseldorf (back when CO flew there), then Cologne, Frankfurt, Munich, and Berlin. Then returned to Duesseldorf. Most of my time was spent in Munich and Berlin.

But you're gonna pay through the nose for your airfare 'cause it's high season.