... those two interval charts on page 23 have me sooo confused. I just can't understand it. I don't get how you use just the 5th and 6th strings to make an A chord at the 5th fret. I see the chart and see where 1, 3, and 5 are. .....
Or am I completely miss understanding this lesson?
Hello and welcome

I think you're misunderstanding the charts - they are to show you where the root note of the *chords* in a key are, not the notes in a chord.
The '1, 3 and 5' are written I, iii and V on the chart: the roots for the I, iii and V chords in a key. You still need to play chords, but using the notes indicated as root notes (by convention: major chords where the Roman numerals are in upper case, and minor chords where the numerals are in lower case):
So the I chord in the key of A (A major) has its root 6th string 5th fret - the popular option is to play an 'E' shaped barre chord at the 5th fret (but you could just as well play a G shaped barre chord). The corresponding IV chord (D major) has its root on the 5th string, 5th fret - the popular otion is to play an 'A' shaped barre chord at the 5th fret (but you could equally well play a C chaped barre chord), etc.
The 'normal' chords need 3 notes, btw, so as long as you can play those 3 notes, you have the chord. (This leads to playing triads and chord fragments which help to add variety.)
Any clearer?
Andy