Hello there,
Glad to hear you are having a good time with ModX. It really is a great community and a great CMS.
To answer your questions, assuming you are using Evo, just log in to your manager (
http://www.yoururl.com/manager), go to "Tools => Configuration => Interface & Features" and under "Path to CSS file" enter well....the path to your CSS file.
As far as to your questions regarding the structure and "assets" directory, this is namely a matter of preference. While it doesn’t necessarily matter where you put things in most cases, I have found that having a common structure for my sites helps considerably when developing. The other benefit to this is that many other developers use this same form of organization, so if you ever take a look at another Modx site, or tutorial you should feel on familiar grounds.
My typical structure goes as such:
CSS & Background images go in "assets/templates/mytplname/" -- This makes it easy to switch from one template to another without sorting through a bunch of images and files from another template. It also makes it easy to move the template to another site.
Content Images (galleries, blog post content, etc..) go in "assets/images". -- This makes them easily accessible from the file manager.
Javascript files go in "assets/js"
You can really create any structure you’d like, however this seems to be the common trend and a logical approach.
Hope this is helpful!
-Jared