This was such a nice message to receive, thank you! : D One of my big goals with Trauma Button is to make a site that's clean and comprehensible, so hopefully that's proof that I'm doing something right, haha!

To answer your general questions:
I have a pretty decent number of years' experience with HTML and CSS. It's mostly stuff that I picked up from years of making custom pages and the like on Neopets (which, to be 100% transparent: I'm still extremely active on) and other pet sites, but: I have been making basic websites for nearly 20 years at this point, and a lot of it is just trial and error (and knowing how to phrase things when you need to google how to do something). You can get a lot done with some templates and some googling, and you'll probably do it in a less roundabout way than I do.

So, I'll split this into two things: actual website stuff that I find useful, and then how I keep myself sane.

Website Stuff and Resources
My actual basic site is set up based on a template layout (the Skyline recreation from here, to be specific: https://goblin-heart.net/sadgrl/webmastery/layouts/ ), then tweaked around to my taste, but honestly, the same creator's layout generator is also just as good of a starting place: https://goblin-heart.net/sadgrl/projects/layout-builder/

And 90% of questions about how to change things up with both basic HTML and CSS, you'll find the answers at w3schools:
https://www.w3schools.com/

Includes are also a must -- they allow you to update a couple files to update every menu on the site. Neocities unfortunately doesn't allow for sever-side includes, which are what I'd normally use, but you can recreate them with client-side javascript ( https://ikewise.neocities.org/includes)!

How I keep myself from going insane
I actually just keep a file on my computer that's just a text document with my entire sitemap laid out in a basic plaintext list, lol. I'm also a lunatic who just likes organizing things (you should see the version of the official art gallery I have on my hard drive).

Generally having pre-defined categories for things (profiles, drama translations, song translations, social media, other translations, information that isn't a translation of a single source, etc) lets me know where any given thing should be, and then it's just a matter of keeping everything in its proper place in subdirectories (like all of the dramas go in the /drama/ folder, all of the character profiles are in the /profile/ folder, etc).

Depending on what you're translating/hosting resources for, there may be other ways you want to organize things; you may want to organize things by medium, or time period, or character, or just vague 'type of thing'. (Like if I were doing translations of a mobile game, I might organize things by main story vs event story vs card story, and then organize THOSE by year or character, etc).

You just want to pick some big overarching categories that make sense to you and that are clearly defined to you; the worst thing is when you make categories so broad that you're not sure if something should go in category A or category B.
(For instance, I personally separate between "other information" and "other translations"; the difference, to me, is that 'other information' is stuff I've compiled from multiple sources, where "other translations" are single-source translations that don't fit into one of my larger categories).

It also helps a LOT to get a second pair of eyes; get a friend to check if things make sense/look good to them, because it's really easy to get caught up in your own flow and not realize that it only makes sense to you.

Then for keeping it updated it's just a matter of getting into the habit; I finish writing a page, then I add it to appropriate directory page, then I update the news page, then I add it to my personal reference document. It's tedious, but it's pretty quick when you get used to it, and once you've got the bones of your site all set up it's pretty painless.

You kind of get a feel for how you want to lay things out by seeing sites that are themselves laid out nicely. I think unfortunately there are a lot fewer good fansites to look at for reference these days, but it also helps a lot to have sites whose structure you can imitate:
-I think The Cave of the Dragonflies (https://www.dragonflycave.com/) is great, even if you don't care about Pokemon; also, her HTML guide (https://www.dragonflycave.com/html-guide) is super useful for helping you to think in terms of semantic HTML.
-It's old and outdated now, but I still maintain that Chris McFeely's Digimon Encyclopedia (https://digipedia.db-destiny.net/) is a gold standard, and proof that you can do an amazing job organizing information without it having to be super fancy. (I spent a lot of time as a kid preoccupied with -mon series, can you tell.)
-You can also copy just about anything you want from phanto.moe except for my actual translations, I'm not super protective of my organization ideas or my code (though my code is a bit sloppy so I wouldn't advise it, lol).

If you'd like any more direct help or have any questions that I may be able to answer, I can definitely give you a hand if you shoot me an email at snakebraining(at)gmail.com.