"Fortifications are nothing more than monuments to the stupidity of man, if mountain ranges can be overcome, so can they." - Gen George S. Patton.

That being said. I would say if you are building a 2 story build your master bedroom where it is at the top of the stairs and your kids rooms are further down the hall away. This will keep you from having to worry about if your kids rooms have been breeched, and it will lessen the chance that should you have to fire a gun in your home that you will be shooting in the direction of one of thier rooms.

Also do not have your bedroom door visable from the floor below, all some one need do is camp out, make a noise and you walk through a choke point and they have you.

This layout has another advantage as the kids get older, it is going to make it very difficult for them to sneek out.

A secondary egress stairway or ladder is a good idea as well, you can bill it to your wife as a fire escape, make it run from your 2nd floor straight to the basement, thus if you have an agressor on the 1st floor, you can get the family downstiars and out of the building with out having to pass them if you have a basement egress.

Make your second story windows high from the floor, if they are more than 12 feet from ground level, a 6, 8 or 10 foot ladder which are the most common will be either impossible or very difficult to use to gain entry to your home.

On your first floor, placing bushes and shrubs with lots of sharp edges or thorns (IE rose bushes or cactus) outside of windows that could be used to gain entry will really slow some one down and ruin thier day if they try.

Think about lighting, companies like X10 make home control products that are cost effective, and will allow you to turn lights on and off with your computer, and with a hand held key fob, think about it, you are clearing your house, you want to enter a room, but you are uncertian if it is occupied, being able to turn on the light remotely is going to startle who ever is in that room and give you a tactical advantage.

Think motion lights as well, they are pretty cheap and low tech, and they will alert you to the presence of anyone outside of your home.

Also having a good DVR and camera system will keep you from having to get out of bed a night, flip on the tv, switch through the camera views, and if there is one where the motion light is on, rewind and see if anything is up.