I had all my wires to the brain box connected and when I finally plugged the harness in the alarm came on. I snipped all the wires down to just the 2nd channel out/in, constant 12 volt, ignition turn on wire, and the siren. Now when I ground either the black or orange 500mA wire the around still comes on. Does anyone know what I'm doing wrong?

Also, what wire on the door lock relay do I tap the Violet Wire: (+) Possitive door trigger Input? Thanks for any input.

I'm stuck on the ones in the list with question marks or if something doesn't look right can you please let me know?
This is what I have so far-

Red Wire: +12V main power -> Red +12V constant (ignition harness)
Brown wire:(+) Siren output -> + red wire from siren
White Wire:12V Parking Light output ->+ Brown wire (behind headlight switch(
Orange/Red Wire: Dome Light relay Output -> - White
Black/Green Wire: 200mA (-) Channel 3 Aux -> remote start input
Gray/Red Wire: 2nd Channel trunk release Power input -> + 12V source
Orange Wire: (-) 500mA Ground when Armed output -> Don't know??Optional ground??
Gray Wire: 2nd Channel trunk release Relay output -> Black wire (button on drivers door)
Black/blue Wire: (-) 200mA Channel 4 Aux -> not used
Black Wire: (-) System Ground
Violet Wire: (+) Possitive door trigger Input
Green Wire:(-) Negative door trigger Input ->Don't know??????????????
Black/Red Wire: (-) 200mA Channel 5 Aux -> not used
Black/Violet Wire: (-) 200mA Channel 6 Aux -> not used
Pink Wire: (-) 2 step unlock / factory disarm output** -> lt. green wire at door jamb??????
Blue Wire: (-) Negative instant trunk/hood trigger -> lt. blue wire in trunk
Red/White Wire: (-) 200Ma HeadLight illimination output** -> Which wire????????
Brown/White Wire: (-) Horn output ->
Yellow Wire (+) 12V Ignition Switch input-> yellow starter wire

Assuming this is for your 92 Bonneville in your sig:

Don't worry about the ground when armed output orange wire.
You either have a positive or negative door trigger input. Use one or the other.
Factory alarm should disarm at unlock/arm at lock. No real need to do this. I don't have the diagram in front of me at the moment, but if the factory disarm wire is negative triggered, you can test by using an inline fuseholder and grounding it out.
As far as the headlamp illumination output, don't use the negative trigger. If there is a switchable jumper, switch it to a positive trigger, and use brown wire at the headlamp switch. You can usually follow the harness down a bit. Test the wire with a DMM by turning the headlamps off and on. At off, should read 0, at on, should read some voltage (usually 11+, but you'd be suprised at what you find on vehicles these days). If there is not a switchable jumper, and you want the parking light flash, use a relay to switch the polarity.

I'm using the "negative door trigger input" since I have my keyless entry tapped into the wires at the door switch and not the relay. The question is where do I tap this wire to? This wire isn't from the keyless entry harness, its from the main harness.

Use the underdash light'* white wire.

I see now. All this time I was thinking that the trigger input has something to do with the door locks :? .

Sometimes yes, it'* the actual trigger that turns on the interior lamps. But, not on all vehicles.

I was reading your post and thought I would lend a hand.

I noticed you said:

This is not good the way you have this hooked up, your Alarm probably won't function correctly like this. It should be wired to the Pink (Primary Ignition) wire in the Ignition harness.

The Orange wire isn't needed unless your doing a Remote Starter and your trying to bypass the the VATS (Factory Anti Theft) or unless your doing a Starter Kill / Anti Grind relay.

The Orange/Red I wouldn't bother with this because when you unlock the doors the dome light will turn on automatically cause its a factory feature. This wire would be used for dome light supervision but its not needed in this case.

Good luck,
Dutch

I do have a remote start already installed, so would I need this orange wire to be a ground? I have some resistors in place to bypass the VATS.

Correct, definately go to the ignition wire, and not the starter wire.