If it confusing you so much, there are other UI mods that you can try.
Reaper's UI, CSP UI...
You also can read through this thread, that explaines pretty well on how to install NewUI:
http://subsim.com/radioroom/showthread.php?t=192374
There are some good tutorials here (even though they are slightly outdated):
http://www.subsim.com/radioroom/showthread.php?t=181538
This video will walk you through the mods folder:
A note though: DO NOT EDIT THE OPTIONS FILE MANUALLY, THERE IS A APP THAT WILL HELP YOU THAT COMES WITH THE MOD - see below.
http://www.subsim.com/radioroom/show....php?p=2012543 - this is a tutorial by Trev on HOW to edit the options.