Spaghetti isn't a huge hazard for HTML/CSS compared to other programming languages, you should see my Python code!

but it can definitely get out of hand. Your code looks fine so far, but it's good that you're thinking about what your organization will look like. Like Adam said above, making use of stylesheets is great! I have all my styles in one CSS file, and I kinda wish I split them up into at least a couple different files instead, as my CSS file is getting pretty unwieldy. Alas I am too lazy to make that change at the moment
I use comments in three ways in my code(
and here is a link to my index page as an example :3 to see my source code, right click -> "view page source")
1. reminders for myself: my memory is terrible! I tend to put little reminders to myself so when I'm reading it back and adding things later I remember why I did certain things, or how a JS script works or whatever.
2. organization reminders: I'll keep little "headers" throughout the code to section off each bit. In HTML this naturally happens as it's all markup with tags, but having titles in comments helps me keep it all more organized in my head so I can more easily find things (for example my little "end header" comment tells me where the actual page's content begins)
3. deactivating code without deleting it! In my text editor (Sublime Text gang), but this is true with most text editors, I can highlight a block of code and use the keyboard shortcut `ctrl+/` to turn the whole thing into a "comment", or turn it back to active code. This is a quick and easy way to test features and I use it constantly when debugging.
Comments are there to aid development, so they are pretty much up to you in terms of content, these are just my own examples and some ideas to share :3 There are style guidelines that professionals need to worry about when working in software engineering, and OOP languages often have specifically formatted comments that can be used to automatically generate documentation, but for a personal site its all up to you! It's your code, comment it however you want
I look forward to seeing what you do with your site