Yes two magnets; as you are using a CDI the timing delay will be wrong as it will think you are going half speed. CDI's have no concept of revs. They only know about time intervals and need to know how long it is going to take for the crank to move from the trigger point to the TDC. With the camshaft going at half speed it takes twice as long and the firing point is then late.
Pete
Not quite true for all CDIs, only applies to ones with auto timing, if you use one from the likes of S/S it will only need a single magnet on the cam as it does not need to know how fast the engine is running and saves wasting a spark.
J