Hi Diana,
Living in Milwaukee, we most often fly abroad out of Chicago. I would say about $800 is average for a flight to a European capital. Sometimes it can be a little less, or a little more, but $800 sounds about right.
I, too, would say take whichever flight is cheapest! Although, you may want to consider if one flight is more direct or not (I'm guessing you'll have some type of layover flying from Chicago to Prague).
The last time we flew to Europe (from Chicago to Greece) we flew Air France, because it was the cheapest. We had a good experience on Air France, and I found the plane to be pretty comfortable. I'm not sure Air France will get you to Munich or Prague.
And I agree--Munich will be expensive in September and pretty crowded, too. I was in Munich with my parents not too long ago around Fest time, and we ended up finding a random hotel, just by showing up. It wasn't cheap, though. If you haven't booked a hotel already, do it soon!