Although as an installer, i dont recomend haveing a remote starter on a manual trans car, there is a good way, and a bad, unsafe way to do it. I recently did my car, which is a 5 spd. If you must do a remote start on a manual, YOU MUST USE SAFETY SWITCHES OF SOME NATURE SO THE CAR DOES NOT CRANK WHILE IN GEAR!!!!! If you dont use any safety switches, you will regret, cause someday you will leave the car in gear..trust me.. Here is what i did, and works great.

I use a DEI remote starer system. These systems have several wires on them to use for connections to safety switches. To disable the clutch start switch, all you have to do is unplug it. A better way to do it, is to use a relay that interupts that switch when the car remote starts, so as that clutch switch works normally. Follow the clutch switch right at the pedal, and follow the switch wires. You will come to a white plug, one end is male, the other end is female. Just undo this plug, and thats it.

Now for safety switches:
I used 2 DEI mercury switches for my install. One switch is mounted to the shifter lever itself, and one to the e-brake lever. This way, if the shifter is in gear, the mercury inside the switch is tilted to not make a ground connection to the wire that needs a ground to start on the remote starter. With the shifter in N, the gound is complete, and it can then remote start. (this configuration only protects from starting in 1st, 3rd, and 5th. You will need another switch on the other side of the shifter lever attached the opposite direction to protect 2nd, 4th, and R) Now the second mercury switch is mounted to the -brake lever. If you take off the center console, you will see a metal round rod that moves with the lever itself; that is what you connect the switch to. So when the e brake is down, it sends a ground signal to the wire at the remote start that shuts down with a ground signal. With the ebrake lever up and engaged, the mercury switch disconnects, and then no more ground signal at the remote start, and then its ok to start up. I will try and get some pics of my switch setup , but its very easy to do, and the hole to mount the shifter switch is already in the shift lever, and i used a nut and bolt to mount the merc switch.

13.5 @108 MPH-2.2 60ft(stupid FWD!)
S16G @ 18 PSI/FMIC/Running on MegaSquirt II (Now with sequential
fuel injection)
My webpage: http://eclipsed4evr.home.comcast.net
-1998 Mitsubishi Eclipse RS-T- "Toy"
-1992 Plymouth Laser Turbo AWD(SOLD)
-2000 Honda CR-V(daily)