Originally Posted by
tom tulpe
Passport control is in FRA (whether or not you'll actually get a stamp seems to vary), customs is in PRG. Bags will be checked through if on one ticket.
And generally customs in Europe tends to be non-issue: if you have nothing to declare and take the green lane, you usually barely notice that you have passed customs. Of course if a customs officer picks you out for a random (or less random based on eg. K9 unit hint) check or you deliberately take the red lane as you want to declare importation of some goods then there will be slightly more time consuming customs protocols.