take the C-major scale for instance:
C D E F G A H C
Fingering: 1 2 3 1 2 3 4 1
Normally, you would pass the thumb under the third and forth finger.
That's called the Thumb Under Method.
If you want to play it with the Thumb Over Method you must put your thumb over these fingers. The serect is, that you must take the third and forth finger off the key very fast in order to make the gap so small that one can't hear it. Pretty hard, isn't it?

Some teacher don't even know about that thing.
I've read Changs book years ago and it was quite helpful in general. But as for playing scales, I must say that I was rather disappointed. He only focused on the TOM and made no explainations how to play scales with the TUM.
However, I don't agree with Chang that you should always use the TOM unless the TUM brings better results ... I must say, that in all cases I could play fast scales with TUM much better! I asked my teacher and she sais you don't really need the TOM but it would be sometimes useful as it bewares your thumb muscles from strain while playing huge scales.
The only pieces where I use TOM (just for practise) is Schubert's Impromptu op. 90 no. 2 and Rimsky-Korsakov's Bumblebee.
regards,
Thi
