1998 volkswagen glx, crimestopper

I am trying to do an alarm on a 1998 volkswagen jetta GLX.  I just moved out of Baltimore into a rural area and someone snatched my pioneer AVI, and riped the amp off of the seat, and left it.  I am really trying to learn/teach myself this alarm install.  1st - When I drive, my parking brake light comes on which in turn cuts my headlights off.  This is an intermitten problem.  I need to troubleshoot but I don't know which relays do what above the fuses.  I don't even know without a shadow of a doubt if its even a relay.  This is my first install of an alarm and my 1st problem with this install.  I have done hundreds of stereo installs.  It has starter kill, remote start, and the vacuum door locks are really getting on my last nerve.  The alarm is a crimestopper 2016.  I am not really understanding all of these aux outputs.  I was also wondering if this BROWN / white wire is only for the driver's door and will I have to run wire to all of the pin switches.  Next, the windows roll down if I leave the key in the unlock position and up if left in the lock position on drivers door.  Is there a way to implement this without a key.  This car is a manual so I was wondering is there a way to wire it so that if it is in gear then it won't let me remote start it.  Also, I don't know the logistics of the alarm.  If it is like any other circuit I have built, can you install one portion of the alarm, check to see if it works, then move on to the next portion; i.e. remote start-check, now door triggers?  I am understanding that these relay (first time I'm actually using one) can serve alot of purposes.  I have read up on the diode uses with the relays as far as back feeding using one output to servel loads.  My question is when is it a necessity and when is it not(diode w/ relay).I am just trying to make sure when I do this install it is done right.  Well I have just about torn the whole dash apart so I am about to go back outside, do some more testing, and depress myself further.  Any time devoted to this topic will greatly be appreciated.  My apologies for the lengthy post.

First you shouldn't need any relays for the alarm portion, second if the remote start is for autos only I can't give you any remote start advice.

As for the factory alarm if it's a black box with two plugs, there is a way to to  kill this and tap door and trunk contacts off it.

The lock wires are in drivers door, if the alarm gives you a way to  extend lock pulse this will raise your windows and close electric roof if you have one (about 15 secs., 10 with four windows and no roof, 7 with front windows only). Extending the unlock should reverse this but you might need a double unlock pulse.* You could use one or more aux outputs set to timed output and join them straight into the lock and unlock wires.

* Never needed to do this.