Well you do use divinity engine 2, it's more than a level editor. To make / modify skills you use the stats editor primarily, which can be opened with the bar graph looking button near the top of the UI. Skills are broken up into a bunch of categories, projectile target shout etc. Right click on an entry and hit override in [ModName]. It's easier to make a new skill starting with a copy of an old one, either rename it to make a new skill or leave the name as is to modify the existing skill.

If you want to make custom visuals you use the effects editor.

So, I figured out what was said, but I still haven't much of a clue how to make it work. I am just confronted with a UI that is full of stuff I cannot comprehend, and I cannot see a full list of the files I want to access, so I have no idea how to work it. I cannot imagine that this is the only way to make mods in this game. Last time I made mods, it was on Rome Total War, and I just went directly into the files and it was really easy to understand. This Divinity Engine II just seems to be an unnecessary level of complexity, but I cannot figure out how to access the files directly. Is there any way to directly access the files, or is the only way through the Engine?

Your mod files are located in three places

GameFolder/DefEd/Data/Editor/Mods/Modname
GameFolder/DefEd/Data/Mods/Modname
GameFolder/DefEd/Data/Project/Modname
GameFolder/DefEd/Data/Public/Modname

You can directly manipulate the stat files in 1 and 4. 1 is the stat files the editor uses, 4 is what is actually used.