I really need to jump into SKSE and understand (at least the gist) of the inner workings of SKSE and Skyrim. I understand how to use the Creation Kit, Papyrus, and I know C++ relatively well but the fact that SKSE is basically undocumented is extremely daunting. The project that I am working on is not something that I can use Papyrus for, unfortunately (I tried).

I want to be able to understand any aspect of the game. I'm willing to read through any manual or book about the subject, but I really don't know what this kind of reverse engineering is called or where to start learning or what base knowledge is needed.

So does anyone have any good starting points? Like information or tips or something on understanding programs and large code bases? Practically anything would help, thanks.

http://www.creationkit.com/index.php?title=SKSE_Plugin_Creation page references a simple guide I wrote to help others get started writing script extensions. It should get you started.

Are you talking about plugins or scripts? Because scripts you'll find on the CK Wiki, plugins.. I can't help you there. Scripts are basically just extension of the existing Papyrus system. If you get to know Papyrus you'll figure it out without any real problems I imagine. As for how the game works its a bit of reading whatever you can find, asking questions, and reverse engineering the rest. Its not something you'll pick up over a weekend however. I'd start by taking a look at the official CK wiki documentation and Cipscis' site regarding Papyrus.