DEI who owns Viper, Python, Avital, etc has this series of actions that need to be done before leaving a manual car and you will remote start it later.

Park car
foot brake down
parking brake up
foot brake up
hit remote start button
take key out of cylinder (car will stay running)
leave car
lock car (car will shut off)

If the car alarm goes off or a door open it takes it out of manual mode and you cannot remote start it until you do that sequence again. Wiring wise the only difference a stick car to an auto is the clutch wire that feeds the sensor the same signal that would be as if you had it depressed. I do the install all the time and if someone asks me to keep it in automatic mode I refuse plain and simple.