FYI, in MODX virtually all constants and variables relating to paths and URLs have a trailing slash (and not one at the beginning). Remembering that will save you a lot of time.
In System Settings, you can use {base_path}, {assets_path}, {core_path}, {site_url}, {base_url}, and {assets_url} (all will end with a slash).
{assets_path}images/myimage.jpg
In PHP code, you can user this form for all the same ones: MODX_BASE_URL, MODX_CORE_PATH, etc.. Again, all end with a slash:
include MODX_CORE_PATH . 'components/mycomponent/myfile.php';
I don't know of any in-depth stuff on the Manager, though this may help:
http://rtfm.modx.com/display/revolution20/Explanation+of+Directory+Structure. It may be a little out of date.
Most of what I've learned about how the Manager works is based on creating a project out of the whole MODX core in a good code editor (PhpEd, NetBeans, PhpStorm) and wading through the code. It's not for the faint at heart.
PhpStorm is by far the best, but it's not free. Once the project exists, you can search for classes and functions and you can right-click on something and jump to where it's declared, even if it's in a different file.
I wouldn't consider, even for a second, working in MODX without a first-class code editor. PhpStorm will highlight any PHP, HTML, JavaScript, or CSS syntax errors, misspelled variable and function names, local variables that are unused, unreachable code, undeclared class member variables and functions, variables that might not be set when you use them (e.g., because they're set in an if() statement), and dozens of other errors that could eat up hours of your time.
If you set up a debugger, you can run the index.php file in the root and trace through the code, optionally with breakpoints, though it's pretty tedious. When you need it, though, there's no substitute.
[ed. note: BobRay last edited this post 12 years, 4 months ago.]