I've been reading up on the Theme Customizer so I can create a backed for the Custom theme I am building. Based on the tutorials I have read, I understand how to enable the customizer, create new sections in eh customize, and how to create and register settings in the database either under theme_mod, which woudl be settings unique to this theme, or options, which would be settings one may wish to have available to other themes.
I also know that you can call get_theme_mod() or get_options with PHP to write values stored in the database into the files for your theme. The problem I'm having is that, all of the tutorials seem to stop there. Unless I'm missing something, they don't go into how you hook the stored settings into your CSS.
My natural inclination is to make a style.css.php file that has the header set to be a CSS style, and move it into style.css using @import. I've looked this up, and I do see some people trying it, however it seems not to be a very common practice.
So in general, I feel like I've some how missed something big most theme developers already know before diving into Theme Customizer.