You're right, it's incredibly confusing, but here's a very brief overview...
Manila is the name of the actual interface that you use on a Diamond or Touch Pro, TouchFLO3D is just the engine that drives it all. So when you're on the Home tab or Favorite People tab, etc, that's Manila.
Manila Editor (as described in Post #4 of this thread) is a PC-based tool that allows you to edit the graphics files that Manila uses.
Diamond TouchFLO3D Config, Diamond Tweak, Advanced Configuration, Advanced Config, and Manila Customizer are all different tools provided by different people that allow you to make specific customizations and registry tweaks that control a number of devices. These are the programs to be cautious of, because they're designed for certain types of devices, but SOME of the tweaks just happen to work for others, so people assume everything works.
So far, the only ones that I would consider absolutely safe for the Touch Pro is Diamond TouchFLO3D Config and Manila Customizer.
As for how to actually customize Manila using these tools... that's what this whole thread is about.
As I'm sure you've noticed, there is a LOT of reading and playing to do, which means that all of this stuff takes a lot of time as well. But as you play around with things, you'll learn what works best for you, and be able to build on that pretty easily.