CAUTION: You will be working with the electrical system in this DIY. When working with the electrical system, it is always a good idea to make sure the engine is off and the positive terminal is disconnected from the battery.
Installing your own alarm system is actually one of the easiest things to do on any vehicle.
I installed the Bulldog Talking Vehicle Alarm, but these instructions should work with other alarms with only some minor modifications. Link to the alarm I'm installing: http://www.bulldogsecurity.com/Products/453055347-model-2030-talking-vehicle-alarm-system.aspx
Before I begin, a bit about how car alarms work. Most alarms have two sensors, a shock sensor, and a voltage sensor.
The shock sensor detects vibrations in the vehicle, such as a bump, shake, or glass breaking.
The voltage sensor detects when the interior lights turn on due to someone opening the door.
IMPORTANT NOTE: If you have a old, weak battery, the alarm will randomly trigger due to variations in voltage. This WILL drain your battery. So, if your alarm randomly goes off when no one is around, time to test your battery.
Note that this install was on a JK, but the procedure is the exact same for any vehicle. I've included a picture of the engine compartment of my MJ for reference.
You want to install the alarm on left or right side of the engine compartment. You *MUST* install the alarm on a GROUNDED metal part of the engine compartment. If the alarm is not properly grounded, it will not work. Do not attempt to attach the alarm to any parts in the engine, only the engine compartment itself. Do not attach the alarm to the hood, as the hood ground wires have a tendency to break (plus the screws sticking through the hood would look really tacky). In fact, while you're in there it might be a good idea to check (and correct) the ground wires. They should be attached near the hood hinges. Improperly grounded hoods could lead to static discharge, and possible explosion if any gas vapors are in the air.
Test to make sure the alarm will fit in the desired location prior to removing it from the mounting bracket.
The alarm and bracket shouldn't be rubbing against any hoses, and definitely should not be rubbing against any hot wires.
Examine the alarm and note how the black ground wire is attached to the mounting bracket. You'll need to reattach the wire later. If your alarm does not have a metal bracket, you'll need to attach the ground wire to a ground screw. More on this later.
Remove the alarm from the mounting bracket, then use the included self-tapping screws to attach the mounting bracket to the engine compartment.
Re-attach the alarm to the mounting bracket, making sure the black ground wire is placed between the lock-washer and mounting bracket. (Sorry, wish I took a picture of this, but you'll understand when you see it).
The alarm should look something like this when you're done:
If your alarm does NOT have a metal bracket, you'll need to attach the ground wire to a ground screw, such as this one:
Test to see if the alarm is properly grounded by touching the end of the alarm's "hot" wire to the positive post of the battery. The Bulldog system says "Thank you" if it is properly grounded.
Remove the end of the hot wire from the battery, then carefully route the wire along the engine compartment, securing the wire so it won't move. I used electrical tape:
Finally, attach the positive terminal to the battery post, then attach the alarm's hot wire to the battery terminal (not the post itself).
Optionally, you can replace the alligator connector with a circular connector and attach the circle connector to the battery terminal. This way if someone does break into your vehicle, they can't simply disconnect the clip after opening the hood. Also, you won't have to worry about the alligator clip working loose this way. I haven't done this yet, but here's an example of the connector.
If you have any questions please let me know.
BTW, for those who note this is a simple alarm...the purpose of the alarm isn't to prevent theft, it is to deter kids from climbing in the JK while unattended, use the car finder, etc. If a thief wants your vehicle, they will take it, alarm or no alarm. Plus, the alarm was a gift, so the price was right!
Installing your own alarm system is actually one of the easiest things to do on any vehicle.
I installed the Bulldog Talking Vehicle Alarm, but these instructions should work with other alarms with only some minor modifications. Link to the alarm I'm installing: http://www.bulldogsecurity.com/Products/453055347-model-2030-talking-vehicle-alarm-system.aspx
Before I begin, a bit about how car alarms work. Most alarms have two sensors, a shock sensor, and a voltage sensor.
The shock sensor detects vibrations in the vehicle, such as a bump, shake, or glass breaking.
The voltage sensor detects when the interior lights turn on due to someone opening the door.
IMPORTANT NOTE: If you have a old, weak battery, the alarm will randomly trigger due to variations in voltage. This WILL drain your battery. So, if your alarm randomly goes off when no one is around, time to test your battery.
Note that this install was on a JK, but the procedure is the exact same for any vehicle. I've included a picture of the engine compartment of my MJ for reference.
You want to install the alarm on left or right side of the engine compartment. You *MUST* install the alarm on a GROUNDED metal part of the engine compartment. If the alarm is not properly grounded, it will not work. Do not attempt to attach the alarm to any parts in the engine, only the engine compartment itself. Do not attach the alarm to the hood, as the hood ground wires have a tendency to break (plus the screws sticking through the hood would look really tacky). In fact, while you're in there it might be a good idea to check (and correct) the ground wires. They should be attached near the hood hinges. Improperly grounded hoods could lead to static discharge, and possible explosion if any gas vapors are in the air.

Test to make sure the alarm will fit in the desired location prior to removing it from the mounting bracket.
The alarm and bracket shouldn't be rubbing against any hoses, and definitely should not be rubbing against any hot wires.
Examine the alarm and note how the black ground wire is attached to the mounting bracket. You'll need to reattach the wire later. If your alarm does not have a metal bracket, you'll need to attach the ground wire to a ground screw. More on this later.
Remove the alarm from the mounting bracket, then use the included self-tapping screws to attach the mounting bracket to the engine compartment.
Re-attach the alarm to the mounting bracket, making sure the black ground wire is placed between the lock-washer and mounting bracket. (Sorry, wish I took a picture of this, but you'll understand when you see it).
The alarm should look something like this when you're done:

If your alarm does NOT have a metal bracket, you'll need to attach the ground wire to a ground screw, such as this one:

Test to see if the alarm is properly grounded by touching the end of the alarm's "hot" wire to the positive post of the battery. The Bulldog system says "Thank you" if it is properly grounded.
Remove the end of the hot wire from the battery, then carefully route the wire along the engine compartment, securing the wire so it won't move. I used electrical tape:

Finally, attach the positive terminal to the battery post, then attach the alarm's hot wire to the battery terminal (not the post itself).

Optionally, you can replace the alligator connector with a circular connector and attach the circle connector to the battery terminal. This way if someone does break into your vehicle, they can't simply disconnect the clip after opening the hood. Also, you won't have to worry about the alligator clip working loose this way. I haven't done this yet, but here's an example of the connector.

If you have any questions please let me know.
BTW, for those who note this is a simple alarm...the purpose of the alarm isn't to prevent theft, it is to deter kids from climbing in the JK while unattended, use the car finder, etc. If a thief wants your vehicle, they will take it, alarm or no alarm. Plus, the alarm was a gift, so the price was right!