Both cities are safe by European standards and ultra-safe by American standards. Just behave sensibly. No restrictions about tripods or photography in public places as long as you are sensible - don't, for example, use a tripod where it might get in the way of people going about their business or try to shoot kids without parental consent.
Difficult to give specific pointers without the innane clichés of the Amsterdam hoors in shop windows and things like canals and flower markets or the Charles Bridge area of Prague. But wander around on foot for a few hours and you will find countless new angles on old subjects.
To get out of the cities, use canal boats in Netherlands or trains in Czech Republic. Otherwise, rent a car and travel freely.