Great topic!! If you are a gun owner and have not thought about this type of thing, then SHAME ON YOU. Here are a some things I teach clients that attend my classes as well as how we handle the situation at home. Just to give a little information on our layout at home, my girlfriends son's room is directly across the hall from ours. This presents a similar situation as to what the original poster was asking about.
1. HAVE A PLAN!! and ensure that all members of the house understand the plan.
2. have a cell phone, and preferably your handgun, ON YOUR PERSON or within easy reach at all times. Phone lines have been known to get cut prior to home invasions.
3. Install an alarm with an audible siren that will still sound if the phone lines are disabled. Even if it doesn't notify a security company or the local police, it will make noise that could end the invasion on the spot. Alarms also have a tendency to wake up neighbors and draw attention.
4. Create a code word or phrase that will communicate to all members of the household that "THE PLAN" is in effect. We use "INTRUDER ALERT!"...very original, don't you think.
5. DO NOT attempt to "clear" your house unless it is ABSOLUTELY necessary to insure the safety of an occupant. Clearing a house with a trained team of SWAT officers is a difficult and dangerous task, do not try it own your own!!!
6. Call 911 and STAY ON THE PHONE with the operator until officers arrive. When they do arrive, follow ALL instructions given. Remember, they do not know you and are coming into a potentially dangerous environment.
As for how we deal with the physical problem of the layout of our house. find a place in the room that puts as many barriers between the entry point and the person occupying the room. This position should also not be in a potential "lane of fire" if possible. Instruct the occupant of that room to go to this point and get as low and as small as possible. In Nick's (girlfriend's son) room, this point is the far back corner of his room. It is away from the door, and not in line with a shot fired from our defensive position in the master bedroom through the door. And our defensive position is arranged such that a shot fired from an aggressor trying to gain access to our bedroom would be fired 180 degrees from Nick's general location. While this does not offer armor like protection, it is easily accomplished with planning, and costs nothing.
Other things we have done include the installation of a wireless, battery powered doorbell in Nick's room, with the button located in the master bedroom. This serves as an alarm should an intrusion occur while we are sleeping. We also own the biggest baby of a Rottweiler you have ever seen. He is useless as far as confronting an intruder, but he does bark at things that go bump in the night. This is my preferred type of dog. My personal opinion is that a dog should be friendly to people, including strangers, as this will allow it to interact with people without the fear of someone getting bit and then you getting sued. Most dogs, even those that are not trained for protection, are very protective of "their people".
Oh, almost forgot to mention...Both my girlfriend and I are firearms instructors and Nick has been well trained and is armed as well. before you think I would encourage someone to arm a child, Nick is old enough to purchase his own handgun and has chosen a Kimber Pro Carry.