What's the best order to learn the various scales and why?

Hi everyone,

New forumer here. Name's Bill. I emailed Pebber a question and he told me to post it in the forums, so here goes:

"I'm just a beginner (haven't even bought a guitar yet), and I've been reading up on music theory in preparation. I understand that basic harmony involves stacked thirds, but I don't understand why that is. Why that interval as opposed to another? I've read there are other kinds of harmony besides tertian, but I still don't understand the reasoning. Could you explain it to me, or point me in the direction of a book or article that could? Also, I plan on reading a number of books, but are there any in particular that explain these kinds of details instead of just brushing over them? I'm looking for something slow, methodical, and comprehensive. Something even a retard could understand."

Thanks in advance for any replies.