A few things:
1) Installing remote start on a manual transmission car is illegal in some states.
2) There are special (kind of expensive) kits for remote start on manual transmission cars. They use what's called "Reserve Mode" and they work like this:
You pull up to where you're stopping, pull the e-brake, put car in neutral, and perform an action (such as throwing a switch on the dash or pressing a button on the remote), remove the key (it stays running because the remote start is reserving the car), get out of the car, and remote lock the doors. At this point, it knows that the following is true:
1) car is locked so no one can mess with the gearshift
2) car is in neutral and e-brake it set so it should be safe to start
3) You performed "the action" that tells the car you will want to be able to remote start it.
Then it shuts the car off. If anyone presses the brake, messes with the e-brake, or opens a door before you try to start the car with the remote, it won't work.