In Germany and Czech Republic absolute majority of trains doesn't require compulsory seat reservation. Reservation is purely optional and most of the passenger travel without any reservation by just taking any free seat. September is definitely not the busiest months, so hardly you can have a situation when all the seats on the train are taken, so I would suggest not to worry about any reservation at all.
I find that there are no reservations possible on Second Class compartments.
What exactly do you mean by "no reservations possible"? German Railways (DB) indeed won't be able to sell you such reservation, but once you in Germany you can buy it easily at any station, cost is 3 euro per person.
Also since you mentioned that there will be traveling 3 passengers, perhaps you should consider option of buying Bavaria-Bohemia Ticket. It will cost 37,20 for three and cover leg till Czech Plzen, while from Plzen you can purchase Czech domestic tickets for 290 CZK for all three, thus making it about 16 euro per person for the entire trip Munich-Plzen-Prague. And the best part is that in Plzen you won't even need to change trains, but continue with the same one that brought you from Munich
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