The manufacturers of roofing materials such as Onduline show how to fix their product:
( http://bit.ly/eaI9Rb if mangled )
They show that you nail through the "crest" or top of the "wave" profile rather than through the trough or valley. To my mind (I appreciate that I must be wrong) that approach seems flimsy; trapping the Onduline between the head of the nail and the structure you're fitting it to would be much firmer if there wasn't a void inbetween, wouldn't it?
I presume the reason for the manufacturer's approach is because the peak stands a smaller chance of any standing water, whereas the valley is where the water will flow when it rains. Minimising the chances of water ingress through the roof is a primary concern, fair enough.
Given that you are told to use "waterproof nails" (or screws) c/o Onduline PP or Safetop fittings, is it really such a risk to screw/nail down via the valleys rather than the peaks?