I am going to talk generalities here. The flywheel should have two marks close together for the front cylinder and another two for the back cylinder. One of the two close marks will be TDC for that cylinder and the other will be firing mark for same.
To determine which mark is which, rotate the flywheel in the direction of normal rotation and the first mark the crankcase pointer comes to will be the firing mark, with the next one TDC. Cams are always timed to TDC. The same will apply to the other cylinder.
Is this what you have?