When the chord chart mentions ninths, elevenths, etc., is there any reason why they could not be the second, fourth, etc.? In other words, does it matter what octave the notes appear in? A ninth is technically an octave and a note above the root of the chord, but it is the same note name as the second. Is it just jazz terminology to use ninth instead of second (I guess so you keep building in thirds?)
You are correct, all intervals greater than a major seventh are infact octave equivalents of smaller intervals. Therefore, a ninth is a second, an eleventh is a fourth, and a thirteenth is a sixth. However, there are certain details to be aware of.
Traditionally, all chords in Western music (prior to the advent of quartal harmony, which is seldom used in mainstream jazz) are built from "cells" of thirds. This is largely a question of spelling, and partially also of philosophy. One of the things to be aware of here is that chords and scales (as well as harmonic progressions) are merely different sides of the same coin. A chord is merely a scale rearranged into thirds. That means that as you extend past a seventh, you continue in thirds to add the ninth, then the eleventh, then the thirteen, until you reach the second octave.
There are exceptions, however. The second, fourth, and sixth are all used in simpler forms all the time. The main difference, however, is that they are used when lower chord tones are not present. For example, you don't use the name "thirteenth" when there is no seventh, you would instead call it a sixth (sixth chords are often used as a replacement from seventh chords, especially major seventh chords and minor/major seventh chords, when the seventh would clash with the melody).
As for the register in which the notes are used, some theorist will tell you never to play extensions in simple position, but to the best of my knowledge, there is no official reason why 6ths could not be played in the first octave of a chord instead of 13ths in the next octave; however, it is generally impractical. Remember that the lower notes are, the more likely they are to clash with other notes, even with notes that would normally go well together in higher registers. How good a combination of notes will sound in the lower registers is determined by how far appart they are, and how low their interval appears in the harmonic series, and how their combination tones correspond to each other. From best to worst, the row looks like this:
P8 P5 P4 M3 m6 m3 M6 M2 m7 m2 M7 TT
(There are a few disagreements here and there, but the overall trend is consistent).
This means that if the root is in the lower bass clef, you might be able to get away with an 11th (a P4, but this is the least common of the three extended intervals), but a 9th (M2) and a 13th (M6) tend to be less agreeable. Alterations to these notes will change this effect, but only slightly (a #9 in the upper regions of the bass clef isn't too bad as long as you keep it away from the major 3rd, but it is pretty unusual to have the bass note so high in the bass clef that this would truly be a #2 rather than a #9). When you add to this the neccesity of maintaining good voiceleading practices, you then also have to consider how the result will sound in the next chord (if thirteenths lead to ninths, then having a relatively wide open 6th in the bass clef may lead to a 2nd in the bass clef in the following chord; generally not good).
Anyway, I am starting to ramble, but I hope that answers your question.
I wish I could point you to a good resource, but there are so few out there. Quartal harmony is a messy subject. The idea is that rather than taking every second note of a scale to create a cell of thirds, you take every third note to create a cell of fourths.
The problem is, theorist cannot seem to agree on how these chords should be interpreted. A typical three note quartal cell might be C-F-Bb, which could be interpreted as a Fsus4, or as Bbsus2, or as C7sus4(no 5), depending on your perspective, while other theorists insist that as a quartal chord, it has it's own identity all together, and should not be labelled with traditional chord symbols. Modern theorists such as Paul Hindemith have created new forms of music theory that could settle the issue, but they have several problems still, and are a very long way from being widely accepted. I suspect it will be at least several more decades before we have a good answer. At any rate, the larger the chord becomes, the more notes it will likely have in common with a familiar chord anyway. Most of the time quartal harmony uses perfect fourths (though some composers also use tritones), and the most perfect fourths that can be stacked at once without creating a tritone is 6. Such a chord would be tricky to distinguish from standard extended chords.
As for typical usage, I would say that in my own limited experience, there are five typical uses. First, there is a single appearance of a quartal harmony within more or less tertian (standard) harmony. This should just be considered as some kind of suspended chord. The second familiar use is to rearrange a passage of chords on a piano or in voice leading so that the familiar triads appear in open fourths as much as possible, though again, most theorists would still consider this to be terian harmony. Third, you can have a passage of non-functional harmony, consisting of a passage of quartal harmony, which would likely defy analysis and sound "out there", kind of cool and unusual, but don't over do it. Fourth, so-called "power chords" in rock and roll are constructed of 5ths or 4ths (same thing), but usually represent standard chords with missing 3rds. Finally, one very idiomatic effect is referred to as the quartal tower; this is very typical on a piano, to play a relatively low note and walk all the way up the keyboard in perfect fourths, keeping the sustain pedal down, so that all the notes ring together; by the time you get twelve notes, every pitch in the chromatic scale has been covered; it is used as a special effect, and once again, don't over do it, or it won't be special anymore.
That is about the best I can do for you. If you want more information, I suggest starting at Wikipedia, their articles on harmony are usually quite good. Good luck!