We are not sure what your question is. Either you wish to create a "through beam" photocell arrangement or have basic questions about the wiring.
You are speaking about an ALGE 5 pin din connector on the back of the cell and the banana plugs. We really need to know if this is a metal RLS1/e photocell or a plastic RLS1c or n photocell.
ALGE has always used the same pin configuration for the din plug.
pin 1 = start pulse
pin 2 = finish pulse
pin 3 = common ground
pin 4 = 12v input for RLS1/e metal cell only
pin 5 = 6v input for all cells
On the RLS1/e (metal) the output banana plugs are isolated from the rest of the circuit by a relay. Polarity does not matter. The 6>20 vdc input gets voltage regulated down to 5v to run the cell. You can connect the cell directly to the timer with the 3 conductor red stop cable.
The RLS1 c (n) cells use the banana plugs to output pulses. Polarity does matter. If the output does not work reverse the plugs and try again, then relabel. The banana plugs are normally used when the internal battery is used. Otherwise use the "red" stop cable or "green" start cable.
You can create a through beam photocell with 2 ALGE cells. Cells designed for this job have the appropriate switches. In a pinch you can accomplish the same goal by blocking the lens with tape. You want the receive cell to only have the "receive" diode active. Block the transmit lens so that the only source of light in the transmitter across the trail.