cribbj, I haven't worked on a Ferrari before, but these are the steps I'd try before doing anything else:
By the way, before you do anything, open a window all the way to both aid in testing, and to prevent somehow locking the keys in the car by accident.
1. I assume this car does have a keyhole in the driver's door, right? Well, start there.
1A. Be sure the hood, trunk, and all doors are closed. Now put the key in the driver's door and turn it to lock the door. Also take note of whether you managed to lock the passenger door too using the key, or if only the driver's door locked.
1B. Wait about a minute. Then, pretend like you're a thief and you just broke the car window. Reach inside through the "broken" window and open the car door.... does the alarm sound?
1C. Put the key back in the driver's door and turn it to the unlock position. Does the alarm stop? Can you now start the car if you want?
2. Repeat 1A. That is, close the car up, lock it with the key, leave it alone for a minute.
2A. Put the key in the door and turn it to the unlock position once. Open the door. Did the alarm sound?
2B. Now turn the key in the driver's door to the unlock position twice. Take note of whether the passenger door unlocks on the second turn of of the key (or maybe on the first turn, or maybe never, but take note of it.)
Here's the idea of what you're looking for: What you want to learn is whether you can control the car's factory alarm system without using the remote. Don't touch the buttons on the remote; just try to control the alarm and/or doorlocks by turning the key in the driver's door.
If you can control the alarm by turning the key, you can most likely find the wires that come off the door's key cylinder, connect an aftermarket system to those, and fully control the factory alarm using the aftermarket remote.
If you can control the factory alarm ONLY with the factory remote, things get a little more complicated. That's when you'd have to start thinking about soldering wires onto the factory remote and burying it inside the dash, or consider to just stop using the factory system altogether and rely on an aftermarket setup....I don't know if I'd want that for myself but it's an option.
Also, are there any other buttons on the factory remote? Just one button for lock/unlock? Any button for panic maybe, or a way to decide whether you'll unlock only the driver's door, or both doors?
If you have any of those options on the factory remote, you could look into a configurable relay like the PAC TR-7. You can set it up, for example, so that it'll only engage if it "sees" a certain pattern on its input wires...........like, say, you'd unlock the doors three times in a row, and the relay will pop the trunk for you.
Also, forgive me for not knowing, but is this car metal or fiberglass or what? How about the bumpers? You could perhaps hide a magnetic reed switch inside a taillight, back window, or plastic bumper cover, then carry a small magnet on your keychain....... pass the magnet over the secret spot and the trunk opens!
And you could probably purposely set it up so that the secret switch will open the trunk but NOT disarm the alarm..... that way you'll have to remember to disarm the alarm with the factory remote first....but if some bad guy figures out to pass a magnet there and open the trunk to get your stuff, the alarm goes off and hopefully he runs away.