OK, let's back up.
The dashboard of MODX and it's path is the very least that you need to worry about.
Bootstrap is a framework, it is not reliant upon MODX, but within MODX you can build your site using standard techniques calling up the Bootstrap files that you need to make it work.
Do not, ever modify the Bootstrap CSS or Javascript files. To override or add styles to your site, create a style.css file and use it as you likely always have. All you want to do is load the CSS files into your <head>, which can be either a full template with the <head> coded directly into the template, or (a common technique) a chunk within MODX that contains the <head> markup.
Best practice is to use a CDN to load the Bootstrap files as you are already doing. This allows you to switch versions easily, as well as take the load off of your own server and pass it to a CDN which improves performance and also makes Google happy.
Go ahead and junk the resource you made with the CSS. Resources are typically reserved to "pages" of your website, or rather any "content" your website may need to call up and display, even if it's not a real "page". This is not to say that you can't put your CSS into a resource, but in my opinion that's way more convoluted and difficult to manage than just loading up a CSS file that can be edited and saved to the filesystem.
Your CSS file, should in most cases be an actual CSS file that you call up in the <head> of your template. Again, this can be placed directly into the template, or as is commonly done a chunk that you call up template. In the chunk would be the entire <head> section as HTML.
i.e.
in your "head" chunk do something like this:
<meta charset="[[++modx_charset]]">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1">
<title>[[++site_name]]</title>
<link rel="shortcut icon" href="/favicon.ico" type="image/x-icon" />
<link href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.5/css/bootstrap.min.css" rel="stylesheet" media="screen">
<link href="[[++assets_url]]templates/currentTemplate/style.css" rel="stylesheet" media="screen">
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/jquery/2.1.4/jquery.min.js"></script></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.5/js/bootstrap.min.js"></script>
<!-- HTML5 shim and Respond.js IE8 support of HTML5 elements and media queries -->
<!--[if lt IE 9]>
<script src="[[++assets_url]]path/to/js/html5shiv.js"></script>
<script src="[[++assets_url]]path/to/js/respond.min.js"></script>
<![endif]-->
<base href="[[!++site_url]]" />
Note that all the files you need are referenced either with a path to your filesystem or a CDN. Often typically the files are stored in assets/templates/yourCurrentTemplate/fileName.fileExtension
Note as well that there is a stylesheet loading that is completely separate from the bootstrap files. Call it style.css, stylesheet.css, or whateverYouWant.css. Override Bootstrap here and add any styles for your site in this file.
In your chunks or in the template, add classes or IDs to the markup and style them within the CSS file itself.
The Bootstrap documentation, and specifically the CSS bits are found here
http://getbootstrap.com/css/
[ed. note: frogabog last edited this post 11 years, 1 month ago.]