Which train internet site is the best to book a train from Prague to Munich, the Rail Europe site or the German Rail Site? Do we need to reserve seats? Does the train have several stops along the way? Does the train go directly into town of Munich? Someone mentioned the bus is the way to travel instead of the train, I'm trying to decide the best way of transportation with out much stress.
IMHO the best and fastest is the bus. It is operated by Deutsche Bahn. It's a double decker with bathroom and snack and beverage service. It goes nonstop from Prague Main Train Station to Munich Main Train Station. You can check Deutsche Bahn website for schedule and price.
Here is a link to the German Rail (Bahn) website. The Bahn bus is definitely the fastest way from Prague to Munich and is direct, ie, no changes. A seat reservation is mandatory and included in the cost of a ticket. However, the walk-up price is 67,40€ (about $85-$90). You can get lower prices, as low as 29€ ( $39), with advance purchase of a non-refundable ticket from the Bahn. RailEurope sells an advance purchase ticket, essentially refundable, for $114. Unless you are willing to book a non-refundable ticket well in advance, the least expensive way is the train. You can buy a Czech Rail ticket from Prague to Germany for 232Kc (about 9€, $12, depending on the exchange rate) and use a Bayern-Ticket from there (18€ + 4€/person). It take about an hour longer and might have one dedicated change (in Schwandorf), but you can purchase tickets on the day of travel.