I'll try to answer your questions in order.
1. Yes; if your son or daughter has a presidential nomination, and they weren't lucky enough to get one of the 100 appointments USING that nomination; (Just like how 1 appointment is given out for a MOC's list of 10, 100 appointments are given out for the many hundreds of presidential nominations); then YES, the non-appointed will go into the "National Pool". CAVEAT!!!! (There always is). I haven't checked the actual numbers or percentages in a long time, but I believe that after all the various "SLATES" have given out the appointments and it's time to turn to the "National Pool" to FILL THE REMAINDER OF THE CLASS; that a certain percentage of the remaining appointments coming from the national pool are from candidates with MOC nominations and another percentage are for those with military related nominations. Hence; another reason for getting as many nominations as you can. The actual percentage of appointments in the national pool per nomination I can't remember. Don't quote me, but I think it's close to 75% of the appointments from the national pool come from MOC nominees and the other 25% come from Military affiliated nominees like Presidential, ROTC, etc. Also; remember, that any appointment from the National Pool; even though they MUST have a nomination to even be in the pool, DOESN'T COUNT TOWARDS THE NOMINATING SLATE. E.g. any appointment from the national pool doesn't count towards a MOC's maximum limit of 5 cadets at the academy. S/He could have 5 SLATED cadets at the academy and hypothetically 10 more that happen to have gotten in from the national pool.
2. The 100 presidential APPOINTMENTS are given out the exact same way, (Most Times), that the traditional MOC slated appointments are given out. The academy ranks the candidates with presidential nominations, and they give one of the 100 to the top candidates. CAVEAT!!! (What else is new). The majority of those with a presidential nomination, probably have a MOC nomination also. In these cases, the academy will TRY to use MOC slates first and save the 100 presidentials until last. This way if they have candidate that has a presidential, they don't have any other, and this candidate is VERY COMPETITIVE and the academy REALLY WANTS THEM, they'll have one of the 100 to use. If this isn't possible, there's still the (National Pool). Also, the presidentials appointment slots are also used when practical for offering VERY COMPETITIVE CANDIDATES and EARLY APPOINTMENT to lock them in before they are accepted at another school. Example: Most MOC's don't even interview until November/December. If an applicant got their application finished in August/September and they have a presidential nomination, and they happen to be part of the "NO BRAINER CLUB" with a 3.95-4.0 gpa; 30+ ACTs; hundreds of hours of volunteer time; 2-3 sport Varsity Letter athlete; Captain of one or more of those teams; also class leader like president, secretary, etc, did boy/girl state, is involved in 2-3 clubs, and academically was in the IB program or did all AP classes; etc... (NO BRAINER CLUB), then the academy will use one of those 100 appointments with the presidential EARLY to get the individual to commit and not accept or even apply to other schools. These are the individuals that NO MATTER WHERE they apply for college; they'll probably get accepted. With scholarships. For those in this same application category who DON'T HAVE a presidential, these are some of the rare few who might receive an LOA and the hope that they'll get a nomination. (Not talking LOA's for recruited athletes).
3. How do you get a presidential nomination. Basically; you need to be the 1st generation dependent of an retired military parent or active duty parent with at least 8 years. I say 1st generation because, grandparents, uncles, aunts, older brother/sister, etc. do not count. Must be the candidate's MOM or DAD who is retired military and receiving benefits; or are still on active duty with more than 8 years. CAVEAT: (Yea, Yea). Presidentials are also open to dependents of reservists. But it is based on POINTS. How many POINTS the reservist Mom or Dad have. I don't have the exact number of points needed. Sorry. The other part of this question is simple. ANYONE who qualifies for a presidential nomination simply fills out a basic letter and SNAIL MAILS it to the Air Force Academy. They verify you are eligible, and you receive a presidential nomination. It doesn't matter if only 50 apply or 5000 apply. ALL ELIGIBLE WILL RECEIVE THE NOMINATION. Doesn't mean they'll receive an appointment. Just means they'll receive a nomination. Hypothetically, if only 75 people qualified and applied for the presidential and all 75 of course received the nomination; and there are 100 appointments given to presidential nominees, that doesn't mean you're automatically going to receive an appointment. You may not meet all of the academy's requirements.
Same thing happens with MOC nominations. There are plenty who receive MOC nomination and even LOA's, but because they aren't 100% qualified, they DON'T RECEIVE and appointment.
Hope this explains your questions. Mike