There is this bus called Flixbus which will take you from Amsterdam to Prague for around 45 euros and vica versa! It will take you 17 hours unfortunately; but the busses are pretty comfortable. You can also take a train from Cologne to prague; and getting from amsterdam to cologne is pretty easy; just check the dutch railways website NS.nl. The train from cologne to prague is a night train called a "sleeper train". This is also a cheap option (don't know exact prices), but not as cheap as the bus; but it will most likely be a lot faster; and vice versa of course
it all about your budget and your vaction , but I brefer car.