main thing you need to do is bypass the ignition sensor on your alarm brain with a relay. you will use the relay as a NC (normally closed) switch inline with the ignition sensor wire on the alarm. the relay will be triggered by the TT. use an output from the TT or even tap into the wire powering the ignition. basically anything providing an output as long as the TT is running the car. if it's a positive output this is how you would wire your relay:

30 - ignition sensor wire (to alarm brain)
87a - ignition sensor wire (from ignition)
85 - ground
86 - output from TT

the basic idea is to make your alarm think your car is off when it is not. your alarm currently does not arm b/c the TT keeps the car running. by putting the relay inline with the ignition sensor wire of the alarm, the alarm will basically see that the car is off (even though the TT is running the car). when the TT shuts off, the relay deactivates and the ignition sensor wire functions normally. thus your starter kill will still work and the alarm will 'see' if someone puts power to the ignition wire without disarming the alarm. if the vibrations from the motor runing gives you problems with the alarm going off while the TT is running you would use a second relay in a similar manner to temporarily bypass the shock sensor (again, when the TT shuts off the relay would deactivate and the shock sensor would return to functioning as normal)

also b/c your alarm now 'sees' the car running only when your key is in the ignition and not when the TT is running it, your doors will unlock when you take your key out of the ignition (as it normally would if you did not have a TT).

-marc