Ok, here we go. THis is the solution to all your problems:
Drop that factory keyless entry and go with an aftermarket alarm. Costs you an extra $100, but is that worth the headaches and pain that you'll save from hiding that cheap stock headunit somewhere else?
As for the wiring, you typically have a permanent 12V wire, a 12V when key is on Acc position wire, a ground wire, an illumination wire, power antenna wire, amp wire, and 8 speaker wires.
permanent 12V = goes to a wire that has 12V all the time.
12V when key is on Acc = only 12V when you have key on any position besides Off
ground = self explanatory
illumination wire = 12V when you have your parking lights on, or headlights on, 0V otherwise.
power antenna wire = controls your power antenna
amp wire = controls your amps/eq/active crossover/etc.
The bare minimum wires you need are the permanent 12V, GND, and 12V when key is on Acc wire.
Illumination is only there to dim your headunit when you turn on your headlights.
EDIT: You ARE doing this with a multimeter right?