Seats can only be sold for the Czech part of the train ride, so what you do is that you buy seat reservations from Praha to Domažlice on the EC362 and then you just remain in the seats after Domažlice. Seat reservations cost 35 CZK at cd.cz.

Thank you so much for your help!

Also also, actually actually - I would highly advise against using this train unless absolutely necessary. I’ve never arrived with less than 30 minutes delay, so any “tight” (less than an hour) connection will not be possible. The train quality is also very subpar, always at least some toilets out of service, the bistro is usually also closed (not that it’s anything to write home about). 

It is very unfortunate, that this is the state of the only rail connection between Prague and Munich - the track is unelectrified for half of the journey, often only single track, Alex don’t have enough locomotives and staff to cover for any malfunction, so they sometimes just turn trains around in Schwandorf/Regensburg. 

This is a very unreliable service, and it is truly shameful.