I've had so much help from everyone here, and being such a newbie I feel like there is not much I can give back. But I thought this little 'how to' might be helpful for some people who want to make a roof for a run out of corrugated plastic.
As I discovered to my chagrin, if you plonk a piece of corrugated plastic on a workbench, and attack it with a jigsaw, you end up with splinters flying everywhere and your expensive plastic cracked and useless!
After some research and experimentation, I found a method of cutting this stuff that seems to work reasonably well, albeit a slow process.
1) Measure carefully and mark out where you want the cut. You will not be able to guide it by eye, as the plastic will bend and warp a bit while you are cutting. If your jigsaw has a laser guide, you can get away with just marking the top of each 'bump', and using the laser to aim for it as you cut.
2) Carefully stick masking tape over the line to be cut, making sure you get good contact with the plastic all the way along (if it is pulled taught and not in contact with the plastic, there is a risk of cracking).
3) Weigh down the work as close to the cut as possible whilst still allowing room for the saw. Make sure the plastic does not hang over the edge of the workbench where you will start the cut, as any vibrations will cause it to crack. If it hangs over the other end, that doesn't matter, you will just have to move it along later so that the part you are cutting is held firmly against the workbench.
4) Start cutting with a hacksaw or junior hacksaw. If you try launching into it with the jigsaw straight away, you guessed it - it will crack. So start it off by cutting a few centimetres with a hacksaw first.
5) Place the jigsaw blade a few millimetres in front of the edge you are about to cut, and let the blade get up to speed before engaging with the plastic. Use a thin metal-cutting blade on a fast setting (not a wood-cutting blade). If your jigsaw has a pendulum feature, turn it off as it will generate a lot more vibration. Practise on a waste piece first if at all possible.
6) Move the jigsaw slowly, especially on the 'uphill' sections. When the blade is going uphill, there is a much greater risk of cracking, and you have to go very very slowly - 1mm per second or less. You can go a bit faster on the downhill and flat sections (this might depend on the direction of the teeth on your jigsaw blade). Every now and then, stop and blow or wipe away the dust, and move the weights further along if necessary - always making sure to keep vibration to a minimum. When stopping mid-cut, wait for the blade to stop moving before withdrawing from the plastic or you risk bashing it and ruining your work.
7) I found it easiest to cut the final 'bump' with a hacksaw starting from the opposite end rather than trying to guide the jigsaw at arms-length - the risk of cracking seems to be greater at the end. Once you've finished all that remains is to remove the masking tape and admire your handiwork.
Any fine detail should be cut with a hacksaw, but following the same principles of weighing down the work and using masking tape. When drilling holes for screws, I also recommend using masking tape, and only drill into the flat sections.
Hope that helps someone! (I know it would have helped me, and saved me a few quid if I'd known all that a couple of days ago!).