first of all, welcome to this Wiki, it's good to see someone else here. Second, I wanted to sincerely thank you for all the edits that you're making, they really help! If you have any questions, just ask :)
the Theme Designer (you can't access to it), that gives general customing options like the watermark (the logo that you see on the top), the background of the site (in this case, the Spirit Animal photo that I edited) and of the pages (this transparent black), the colors of links and buttons
the Wikia.css, with whom you can customize and design almost everything; but you first need to know what the codes are, so
source of the page (ctrl+U)
and click on the first loooooong link that ends with "Qualaroo.scss" (here you have ALL the source codes)
right click on the thing you want to customize on the page
try to see the class="..."
copy the ...
ctrl+F (search function) in the source page and paste the ...
copy all the code like ".WikiNav .subnav-2" and not only ".subnav-2"
and then, you just have to try until you get what you want