This has probably been asked before but here goes anyway. I have a Humminbird Helix 10 with the Mega transducer mounted to the outside of the boat and thru the hull transducer. Both are connected by a Y cable. Is there a setting on the head unit that needs to be set or better yet can someone explain how it works?

No settings, the head unit sees both transducers as one. The way the Y cable is pinned out is that the si transducer will only transmit si/diand temp to the head unit. The thru hull will send 2d to the head unit. so the 2d element in the si transducer does not ping, only the thru hull transducer will ping for 2d reading

How does the head know which transducer signal to display if they both transmit?

The head unit will display si di and 2d. The si and di will come from the si transducer, the 2d will come from the thru hull. The head unit doesn't decide, the y cable splits the signals up in such a way to where the head unit will read both transducers as if it were one si transducer.

The Y cable is wires, the 2D piezo in the SI transducer is DISCONNECTED (no wires) and the added 2D transducer is connected in its place (wires). The plug that connects to the display is the same for the Y cable and the SI transducer.
It is impossible to get 2D/Depth from the SI transducer using the SIDB Y cable==no wires.

I contacted David at Shut Up and Fish, he explained exactly what I was looking for.