one thing to keep in mind is that there are two events in play here concerning these marks. the bottom gear will reflect the position of the piston and when it is at true tdc, the twin marks will be in direct alignment with the centers of the crankshaft and the camshaft. proper timing will be achieved when the chain is attached while the camshaft lobes are exactly aligned with the top level of the cylinder ( made easier by later gears having two punch marks to align with). to have the crank mounted balancer in the right place, the single mark on the lower camchain gear (counterbalancer shaft) should be aligned with the twin marks on the crank gear (that's what makes the motor so smooth ;.), and since the crank and balancer gears are the same size, the relationship stays the same as it rotates.
clear as mud, right?