Okay, I read your whole original post and a few others (but not all). I'll throw in my opinions as a former electronic security technician and infantryman, both of which are obviously security oriented. Bear with me, I feel good finding a question on here that seems to be aimed at me...
The house you described is the perfect target for burglary. Most crooks aren't home invasion types (not that you shouldn't prepare for them...) they would prefer you are not home. What you described sounds like they are "casing the joint". Could be your family's home, could be the neighbor's. That you have identified them and approached them may have foiled this plot. You did the right thing, you and your dad. Take a picture of the if you can. If they object, tell them it is a free country and walk back inside.
The security system WITH cell backup is great. This is your main line of security before it gets bad. This means the locks have been breached. You have the 1. the front gate/entry, 2. house doors/locks (physical security), 3. alarm system, 4. deadly force. Radio is better, but cell will suffice just fine (radio is better because it depends on NO land lines --cell phone networks still need a land line, which usually fail in dire emergencies, and these emergencies give the bad guys sufficient cover to do their deeds --think Katrina). Now the security system is no good if you don't know how to use it. That system will do a lot more than arm and disarm. You should get an alarm technician, not a salesman, and preferably the tech manager, to come discuss the features (many of which they don't tell the average customer about for reasons of mitigating false alarms --most average homeowners will never use more than arm/disarm anyway). For instance, it can be used while your mom is inside or outside (ask them, too difficult to discuss here, but it has to do with split arming/partial arming) and having a wireless keyfob is nice. You can arm/disarm, call police, fire, ambulance,..., even turn lights on and off with one of those. Finally for the security system, make sure to install an exterior siren or bell (bells are louder if you get the right one) and a strobe light. Any color is fine, but I prefer blue on the outside and white on the inside (if you choose to use one inside --it can disorient the intruder who isn't familiar with your house, but it can disorient you too if you aren't careful, and it can impede aim). An interior siren is useless alone. It can alert you and it will make the bad guy's heart race faster (seriously, for good and bad) but your neighbors, no matter how close, will not hear it, and so the bad guy will not be too worried about that (and a quick blow with the crow bar used to breach the door will shut it up nicely). If money is no option, then there are myriad lawn defense (passive only in US --SA used to allow user initiated land mines, not sure about now) measures that will give early warning. If money is an option, just make sure you add the exterior bell at minimum. If you do that, provided your system is wired correctly, you should have a very similar system to that of a bank. Now you can add cameras, but cameras are useless "right now". Cameras are good for the aftermath and for identifying a criminal after the fact. Cameras as a deterrent are okay, but they really shine afterwards. You should advertise the fact that you have an alarm and also cameras (whether or not you have them). I advertise this on my front gate right next to the "posted: no trespassing sign". If you do go with cameras, make sure that they are installed "out of sight". Advertise the fact you have them, otherwise they are not a deterrent at all, but don't advertise their locations. For instance, a cheap looking alarm clock camera is better than your typical dome camera in a house. Oh yeah, make sure your alarm has a duress code, and that it is not "1234" or "2580". If you don't understand this, you NEED to have that tech manager come out soon. Use a number that is easy to remember but not easy to confuse with the usual code. This needs to be an number that you will remember with a pistol to your head.
A lot of people mention dogs, but dogs are iffy. Unless it is the right kind and trained, it will not be that good. They are food driven, and if you get just any old kind of dog, peanut butter and phenobarbital will put the biggest dog out for the night. Not even a whimper. They are too easy to bypass. But, in combination with the alarm, lights, etc., they do help. Just don't depend on a "junkyard dog". Trained Caucasians are a good deterrent --they are very territorial and can be very aggressive. But remember that peanut butter and phenobarbital will still knock them out silently unless trained NOT to accept food from strangers (which can be quite difficult). When I installed alarms, I would have people tell me that they didn't need them because they 1. had a dog and 2. they were armed. I reply that does you no good if you are asleep and the dog is too, albeit a drug induced haze or otherwise, and you have no warning. Depend on the alarm for warning (provided it is installed right). Don't depend on the dog. The dog is an added layer, just like the cameras and lights. The firearm is the last resort.
For where to hide during a break-in attempt, I would advise looking at the layout of the house from a tactical perspective. The bathroom may or may not be the best location. How will they get in? Where will they go? Is high ground the best? Can you easily shoot them, but not them you? (If you have an upstairs, catching them ON the staircase is good because they are unbalanced and in an awkward position. Plus they will fall harder if you hit them on the stairs. Is this a possibility?) They will probably enter the entry with the least exposure and difficulty. Make it difficult (I didn't discuss physical security, but perhaps I should below). When they get in, make sure there are no useful or visible weapons (and certainly no more powerful weapon than you have yourself) between you and the entries, i.e., keep the weapons in your retreat. I won't go into the shooting scenario, that is tempo based anyway, just try to analyze the situation while you have the luxury of analysis.
Physical security. Strong windows, locks, etc. Steel doors are great, but if the frame is wood, you might as well get a cheaper door so when they kick it in it will cost less to replace. Use steel frames, even with wood doors. The frame and the lock are the weak spots, so make sure those don't fail. Remember the area of the door that contains the lock too, because if that fails, none of the rest matters. I saw a episode of "Cops" where a cop was trying to kick in a wood door. Must have had a good lock and a steel frame on that wood slab door, because the kid trying to kick it in couldn't --he got winded after about the tenth try. I missed the rest, but I assume the got in eventually. Doors and locks don't keep people out (most of the time) but they do slow them down considerably and do make a lot of noise. Oh yeah, you should be making noise too. Like "the cops are on the way" and "I have buckshot aimed at your head right now", etc. For windows, well, they are windows. Short of bars, there isn't much you can do (unless money is no option, then get laminated glass with glass on the outside and polycarbonate or lexan interior layers --get glass on the outside for cleaning and scratch prevention). The stick in the sill and heavy duty lock are useless if you have glass panes and thin frames. What is useful, and my grandmother used to do this, is to plant large thorn bushes under the windows. Get the right ones though, your climate my dictate, but the ones that have large, 2" wooden thorns work best. Very painful. Kept my dad and his siblings from sneaking out at night too.
Well, there is a lot more that could be said. Security is a work in progress in my book, and any work and changes take that into mind. I don't worry, as all this may suggest. In fact, I sleep better knowing that it will take an act of God to sneak up on me in my house.
At an absolute minimum, make sure mom knows how to, and can use, that shotgun. Test that alarm system regularly (learn how to do it without setting off the exterior bell/siren --neighbors will ignore it if it goes off all the time). Do some dry runs to test out your strategy, and do it again and again so that it becomes second nature. I hope this helps, and I hope you never need to use all of it.
