Well, if you were not so Foole-ish, you'd notice that the notes do go up as you go right in my chart. This corresponds with keyboard layout. But if it makes more sense to you the other way (which is counter-intuitive, to me) by all means, flip the chart and the directions.

Whether you go left or right depends upon what you have and what you want to find out. So some of the time, you'll be moving contrary to the pitch progression of the chart itself. I indicated a couple cases of this above. If you want more explicit charts, they can all be derived from the half-tone circle as given above.

To most people, it is natural to talk about going "up the neck", which is actually starting at the nut (the highest physical point, as the guitar is held) and working physically downward toward the bridge. This is because the nut is usually considered the bottom pitch-wise, and all fret numberings proceed from it. (Oddly, the strings are numbered in reverse, with the lowest numbers being the highest pitches, and proceeding right-to-left from the visual standpoint!) I didn't make up these conventions, I just follow them. If you want to argue, you've got several centuries of musicians entrenched on the opposing side.