Mystikbrian,
If you use clear PVC flexible duct like that version that ClearVue supplies with their cyclones, then the bin sensors could be placed so they transmit their beam through both segments above the bins. A true "Y" would be needed (versus a wye as provided by plumbing pipe which is straight with a 45 degree segment). Assuming that the two bins will fill at roughly the same rate, the first one that blocks the sensors would set off the alarm and, (assuming you make the interconnection) if the Normal/Bypass switch is set to Normal, the cyclone would be shut down. I have tested the sensors through two sections of flexible duct and the signal is fine, as shown in the attached photo (this shows the older version of the sensors, but they are equivalent to the newer model I provide).
I will set up a bench test that uses two sets of sensors to see if one bin sensor control box can detect inputs from two sets of sensors. I'll report the results back in this thread.