05 scion xb, factory security sytem

I have searched the boards here and didn't see anything, so my apologies if it's been asked (a link would be appreciated). I have an 05 Scion xB with the factory security system. I *believe* that it has ignition cut-off if the alarm is triggered, however the only way that I know of to trigger the alarm is to open the door while the system is armed. This has an obvious disadvantage that became all too apparent the other day when the car was broken into. The thief broke the back door window, then reached in and unlocked the doors using the drivers door switch, thus disabling the alarm. Unless someone saw or heard the glass breaking, it would never even draw attention. Long introduction to get at my questions I know, but I thought it beneficial to qualify my concerns and questions. First question: When installing an aftermarket alarm, can it be used in conjunction with the factory system, or should it just be completely removed and allow the aftermarket system to handle everything? Second: Can anyone tell me where the factory system is? Third: Is it possible to create/buy a circuit that will disable the inside door lock switches during/following an alarm trigger? I would be happy with one that would disable them only while the alarm is actively triggered, but one that would completely disable the door locks after a trigger would be even better. Fourth: I'm also considering mechanical deterrents as well, but am concerned about the possible safety implications that would have. For example, what makes it harder for a thief to gain entry could also make it difficult for emergency entry/exit. Any thoughts related to this for: security film (shatterproof film), removing/disabling the mechanical locking knobs, slim-jim plates, etc? Finally, thank you for such an informative website. I have learned a lot in the short time that I've been here and hope to learn a lot more!