1997 Chevy Silverado Car Alarm w/remote Start
When anything is "Negatively Triggered" this means that usually that, that Circuit, has a resistor of say 10K Ohms, to the Positive Voltage rail. To "Signal" that it is to be "Active: the Circuit is "Pulled Low" by a short circuit to negative/ground. This then gives a negative going signal, that's detected, and the Action performed.
Now usually any Inputs or Outputs have these Pull Up Resistors on the circuit board, and the simple grounding of the wire will "Switch" the Input. So to operate this we would install a switch, with one end on the wire, and the other end wired to the Negative/Ground, when the switch is tripped, it puts a short circuit on that Wire, and in turn, it will operate whatever is operated when that particular switch is tripped.
Most Often an Output is "Tied High" or left alone, as usually the "Logic: of that wire, High or Low, +Voltage or -/0 Voltage, is handled by the electronics internally. You can tell this by measuring the Voltage to earth when the unit is powered up, but not connected. High Out/in puts will have a +12 V voltage on it, or 0V on it. Toggling this line the "other " way activates that wire. If NOT used it is usual to "Tie them high" unless told otherwise.
All/Most Inputs and Outputs aren't needed for actual operation, and can be tested by Tying Inputs & Outputs high or Low, to activate or test a function...
A flame out relay, most likely wouldn't be used, unless you were wishing to monitor for Flame etc. (Sometimes used when running nitro)
Also I find a light bulb on the end of a pair of wires invaluable when testing inputs and outputs, using a small Bulb, you can use it to see an Output or to Trip an input and a visual indication is a lot better when testing
It seem that you do have a good understanding of whats going on, hope i haven't confused you too much and have been of some help..
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