i was dealing with a bad battery for a awhile before getting it replaced so i was always jumping my truck, and as soon as i would attach the other the truck the alarm would go off, scares the crap out of you the first time it does it, but i would just have the key fob ready to unlock the truck and the alarm would stop. it only seemed to happen to me when the battery would die will the doors where locked. so have the key fob handy to unlock the truck and you should be good to go.
one other issue i had jumping the truck is if you short across the battery you may blow the the throttle positioning fuse which will put the truck in limp mode. Drove the truck 7 miles at 9 mph and paid 115 dollars for the dealership to hook up there computer to replace a 30 cent fuse to figure that one out.
If the alarm goes off with the immobilizer system, you shouldn't be able to start the car until the unlock button on the key faab is pressed, which deactivates the alarm. For the early model "red button alarms" (a small, red button that serves as manual disarming), you can call a dealership and they can walk you through the process of disarming the alarm and letting you start the car.