Shane,
Most "legal" installers won't do a remote start system in a vehicle equipped with a manual transmission.
However, friends always seem to hook us up, whether it's a good idea or not. (One of my installer buddies has a brother that does garage door repairs ... you do the math ... /ubbthreads/images/graemlins/wink.gif )
At any rate, seeing as how you're going to performing your own install on a manual transmission equiped vehicle, you will have to defeat the clutch pedal interlock. (aka unplugging the clutch switch )
Once this is done, the car will turn over on the starter when you request the remote start feature.
That's great to warm up the car on a frosty morning...
... not so great if you just "pocket dialed[/i] the alarm while rubbing up against betty lou in a romantic fashion...
Since you live in the bay area, it is inevitable you will be parking your car in gear at times to hold it on the steep ass hills you guys got out there.
There's not a lot you can do about reporting the shifter position to the alarm ecu without getting crazy with reed switches and the like, so sooner or later, you're going to run into trouble. (I know I have in the past, /ubbthreads/images/graemlins/blush.gif several /ubbthreads/images/graemlins/blush.gif times /ubbthreads/images/graemlins/rofl.gif )
After awhile I learned to throw a few safegaurds into the system.
Many times, the system can be programed to require a very specific sequence in order for the remote start to be enabled.
My favorite is to require the owner to set the hand brake, leave the engine running in neutral, exit the vehicle, arm the alarm system, and then press the remote start button once, killing the motor.
This will shut the engine off in a safe condition and prepare the system to be remote started with no chance of the vehicle being in gear. ( I use two pushes with a pause in between to signal the system to start)
As long as the alarm is not cycled, the system is prepared to be remote started with very little chance you'll be explaining to your insurance agent what happened to your garage door.