The button set up kind of makes sense to me. If you put your DS sideways, the Y button is the closest to you, and it represents the lowest fret/notes on the guitar neck. Red and yellow are X and B in the proper left to right positions. And the A button is the furthest away from you, so it is the blue fret, which is the highest note. So it makes sense as a matter of lowest pitch to highest pitch, I think.
It is not logical in the sense that, on a guitar, the higher notes would actually be closer to your body (ie you would slide your left hand to your right, closer to your body, in order to reach the upper frets).
I can do chords just fine. Hammer ons and pull offs are a bitch though.