Hey, sorry I haven't been on here for a few days. Framingham is nice; I have some friends who live out there. I also have a lot of Brazilian friends; they tell me you have lots of good food in Framingham!
Anyway, to answer your two questions:
1. Arm wire. It doesn't hurt that you connected the arm wire, but it also doesn't help. When the Civic is running, the factory alarm can't be armed.
Basically, whenever you remote start your car, the situation is this:
---The car itself is still theft-resistant, because the steering wheel is locked, the car can't be shifted from Park without depressing the brake, and depressing the brake kills the engine anyway.
---However, if someone wants to break into your car and steal your personal belongings from the interior, the alarm's never going to go off when they break in. Not a big deal for most people.....but yes, your car has no factory alarm when the remote starter is on.
---How often do you ever remote start the car, but then not get in and drive it? As in, you activate the remote start, but then you decide to stay home instead, and you turn the remote starter back off by remote, or you just let the runtime end?
If you want, you could connect the BLACK/ red "pulse after shutdown" to the car's arm wire......... that would rearm the factory alarm after the remote starter times out or is shut off.
2. Parking lights.
---Short answer is, I'm sure you're just fine and won't break anything.
Examples: Altimas and Maximas have the radio and HVAC panel go dark when the positive parking lights are hooked up. 2001-2007 Caravans have no dash lighting come on at all if the positive wire is used.
---Longer answer:
A. The switch makes a low-power ground when you turn it on.
B. That negative signal goes to some place(s) in the car that vary from car to car.....I'm going to guess probably the BCM (Body Control Module), which is likely part of the fuse box on your car.
C. The BCM takes your command with the switch, and does various things with it: Lights up the dash panels (based on the position of the dimmer switch), and lights up the outside of the car. Many Mitsubishis and European cars even have two separate left and right parking light wires.
So anyway...... you've basically gone around the BCM and powered up the lights by yourself, just like the BCM would have done if you turned the switch on.
Imagine ordering a pizza, but then having your friend pick it up for you instead of having it delivered. You've "jumped around" the delivery driver by having your friend do it, but it's still the same pizza.
The only thing you haven't done is supplied the correct signal(s) to activate the dash lights.
Theoretically, I guess you could, if desired, try to figure out what triggers the dash lights, at what brightness, and duplicate that with relay(s) and resitor(s) and whatnot...... but at that point it'd be easier to of course just use the negative light wire at the switch.
IN SUMMARY: It's probably best to duplicate the car's factory behavior whenever possible, which would be to try to duplicate what the light switch does..... which would be to trigger the negative wire at the switch.
However, there are so many cars where the negative wire is difficult to access (2003-2007 Accord), runs by data that we can't easily interface with (Nissan, Mitsubishi), or needs inline resistors (many Chryslers), that we installers just grab the positive wire as it saves time and energy....and it works fine anyway.