You may already be aware of this - but in case the OP or others aren't - bahn.de actually offers two ways to adjust the connection times. Using the 'Further search options' or 'Change other data' options, you can:
a) increase the 'duration of transfer' (to say, 15 or even 30 minutes) - useful if you know you're going to be slow moving at every transfer (eg: due to heavy luggage or a large group); and/or:
b) require a minimum stopover duration at any particular point, using the 'enter stopovers' option - useful if you want to have a stopover in a certain city, or ensure sufficient time before a 'can't afford to miss it' train (such as an overnight sleeper).

On the currency issue, Strawboy1230 should note that of course, Prague isn't in the eurozone either (although again, I think many places will still accept euros, although possibly at an unfavourable rate).