If you dont have any marks on the alternator you are going to have to make one so you can time it properly. If you don't alredy have one, you need to get a crankshaft timin pin that should locate the crank at the exact firing point so you can make a mark near to the timing pointer in the primary chaincase.
If you can't see the coils when the back plate is fitted you should be able to hold it up in the middle of the slots as Brian suggest and scribe the housing at their rough position. Take the plate away and should then be able to line up the trigger roughly and tighten it lightly before finally offering up the plate. That should be good enough for it to run so you can get a strobe on it. If you run out of adjustment on the slots you may need to move it slightly but hey thats the joy of playing with a Bonnie!