Photo courtesy Wikimedia
A good starting point is to download the map of the Dutch railway network. It's a PDF file. Click on the map below to download.
The Dutch railway company NS has a site including a journey planner. It is quite good and will take schedule deviations due to scheduled maintenance into account. At present it's in Dutch only..
If you need also tranportation by bus, tram or metro, you can use the public transport journey planner. It is more extensive, but sometimes it creates complicated proposals with many changes, just to save a few minutes. A major advantage is that you can print a simple map of the route from the stop to your destination. It requires some care to select the best scale to print it.
Arriva has an English language site where you can plan your trip.
The other regional railway companies do not have websites in English.