pin switch for tonneau cover

I just installed a remote starter/keyless entry system into my truck, and I was wondering which wire should I use to hook up a pin switch to my bed cover?  Would it be best to hook up to the hood pin wire or the door trigger input?  My door trigger wire on my alarm is a negative input and so is the hood pin wire.  I have the door trigger wires from the vehicle diode isolated at the BCM and when they connect to the input wire.  I would prefer connecting it to the door trigger input because this would still allow me to remote start with the tonneau open, but I know it would be tricky to figure out the wiring with all of the diodes.  If someone would be able to draw a good diagram for me, I would really appreciate it.  Nothing else is connected to the hood pin input besides the hood pin.  Would I need to diode isolate the two pin switches, or should they be alright if that is the best way to go?  I am just looking for some outside opinions.  Thanks

Your system does not offer a trunk pin input?Installer, IT support, and FFL. I need less hobbies.