To best intuit how the coordinates work, it helps to do some hands-on experimentation:
[*]Make a macro of the /loc command, so you don't have to keep typing it.
[*]Find a flat, quiet area to stand in. Check /loc to get your coordinates.
[*]Move directly in one of the four cardinal directions — north, south, east, or west — for several steps and check /loc again. Note which part of the coordinate changed, and in which direction.
[*]Move directly perpendicular to your previous movement (e.g., if you moved north previously, now move east) and check /loc once more. Again, note which coordinate changed, and in which direction.
[*]Jump (or fly) straight up and hit that /loc macro while in midair. Once more, note which coordinate changed, and in which direction.
By understanding how the change/difference in values in the coordinates translate into general directions, you can then adjust your position to line up with the target coordinates, one axis at a time. ("hmm, my x-coord is slightly higher than the x-coord of my target, while my z-coord is way lower than the target's z-coord; that means I need to go east a little bit, then south a whole lot")
You might also find this ParagonWiki page useful in visualizing how the coordinates work.