File Structure in EE

On some sites I start at "default.site" directory as my root. Saves lots of clicking/expanding.

This is an old post, but since it was bumped to the homepage, I'll add my 2 cents.

Your assets folder can be where ever you like. If they are public assets you can keep them organized in your web root as is common practice. They do not have to be stored in your templates folder, or within your ee system folder.

I'm not 100% what your asking when you mentioned "I'm just confused on all the other junk in the way." But if it helps, the 'default_site' folder is just that, as ExpressionEngine, via MSM can host multiple sites from one install, so there needs to be a way to identify them in the file hierarchy. You can change the name of your site in the CP from 'default_site' to what you prefer. The 'blog.group' folder indicates your template group as you see it in 'Template Manager' within the CP. It would translate to the path/url yourdomain.com/blog/index.

Yes and no.

No, you can't totally reorganize the system/user/templates structure - ExpressionEngine needs the basic filesystem layout to be in place in order to work.

Yes, you can do as you please in your template directory (it looks like you are using default_site). You already have a blog.group directory, so you can make an assets.group directory along side of it to store your asset files. Any other template files you create would reference your asset files like this:

<link rel="stylesheet" href="{site_url}system/user/templates/default_site/assets.group/style.css" />

For what it is worth, I am in the habit of moving the system directory above the document root and creating a symbolic link from the document root to my template's asset directory, like so:

css -> ../system/user/templates/default_site/assets.group/css
fonts -> ../system/user/templates/default_site/assets.group/fonts
img -> ../system/user/templates/default_site/assets.group/img
js -> ../system/user/templates/default_site/assets.group/js

This makes the site a bit more secure and makes asset pathing cleaner.