I think since there is only one set of points (one points unit) on that bike than it must do both cylinders.
I believe on those bikes, the entire points plate is rotated to adjust the timing, which is individual of the screws which hold the points assembly on the plate. Like the SOHC/4's, you set the point gap first, then move on to timing.
Moving the plate must adjust the timing since it changes the moment at which the points open/close. I've never used a strobe light for adjusting timing on these bikes before, I find it much easier to use the static method with a little static timing light unit I built with some wire, alligator clips, a battery and a wee 12v light bulb.
To use the strobe light, I believe the engine needs to be running, and you point the strobe at the timing marks and look for the marks to line up. HOWEVER, since these have a mechanical advance unit, you either do this at a low RPM to make sure the advance unit is in the retarded position, or at a higher RPM and use a second set of timing marks if the Bike is equiped with them.
Point gap or worn points changes the timing quite a bit, so start there when looking for problems. A stuck advancer unit (located behind the points assembly/plate) will also cause problems because it wont allow the timing to return to its normal position for timing.
Matt.