Here`s the deal with flute acoustics--
First a quarter tone is something in between the standard half steps you find on a [in tune] piano. So sounding a note halfway between the E and the F is one example. Likewise between D and D#, between Ab and B, you get the idea. Usually there are little arrows on the note`s stem indicating up or down, telling you whether to play a quarter tone sharp or flat of the note written.
Second, by playing with acoustics etc. you CAN make two notes sound on the flute at the same time. The physics that go into flute sound include overtones or harmonics. Some advanced flute music will actually include these by writing the note in parenthesis above or below the note you are actually supposed to hit.
Everytime you play a note, you will be playing more than just the fundamental frequency, but the harmonics usually blend together causing what people refer to as a "rich tone." There are ways to make these come out more. Even when I try to hit the notes just right to make the harmonic heard, it`s usually accidental when it works.
If you are particularly interested in this phenomenon there are some good books available- The complete guide to the flute by Burkart and Phelan has a good introduction to the physics of sound of the instrument without being overwhelming. This is their website:
http://www.burkart.com/book/book.htm
Don`t bother buying it though, find it at the library (if yours doesn`t have a copy, you can usually have it sent over from another branch)
From there you can start poking around your local university`s music section and see what interesting things you can find.