Lance - normal is to have the TC(s) nearest the camera body and then the tubes. That way you get the full TC effect on the magnification from the lens and ext tubes- so your #2 example is correct.
I expect I will be buying a tube kit in the month and half. My bday is in early March, and the in-laws are buying me a 1.4 TC, so I will most likely buy the tubes around that time.
With the tubes behind the lens, you simply reduce the close-focus point of the lens, thereby increasing the image size. By adding a TC at the camera end, you increase the effective FL of this close-focus set-up.
Putting the tubes between the TC and camera body is much less effective, as the tubes increase the image size by lens FL/extension (in mm). A 50mm lens on 50mm extension yields 1:1. A 50mm lens on a 2X TC is effectively a 100mm lens, and, on 50 mm of extension, yields 1:2, or one-half life size.
You will lose plenty of light with this set up, but it works great and I use it frequently (being a poor, MPE-deprived Nikonian).
