Spot on Disciple. There's so many choices of media to use and different ways to stack it - and they'd all work. We aim for long service intervals and to that end we want coarse mechanical first in line. We also aim for optimum conditions for nitrification and that means keeping the bio media clean, somewhere near the end of the line. The most important thing is that it all keeps flowing well to supply oxygen to that biomedia.
Neo, stack it how it works out best for you - you can change it later if you're not happy. I have presumed you've got only the supplied media and some marinepure handy but perhaps you have more. I don't disagree with JayC or Disciple's advice, I just don't consider it to be making the most of what you have. While I don't use it I fully accept that marinepure is awesome media, but substrat pro is being underrated here. It's awesome stuff too. So is siporax, biomax, matrix and a bunch of other excellent media with other brand names.