Yup, you need to set things up correctly - there is no wasted spark, they're alternate sparks one at a time. So the mag has to be set to fire the piston that's on compression. Some people prefer front pick-up to the left, others to the right. I set my bikes 'rear to the right' every time so I don't have to think about what's what on any particular machine.
To save having to peer into the gloom looking for the brass bit through a pick-up hole, the rear (gearbox side) pick-up on the mag is fired by the lower lobe on the camring, the engine side one by the upper lobe.
But even if you muddle up the pistons, swapping the plug leads when it won't start should solve things.