Should I use `get_stylesheet_uri()` or `get_template_directory_uri()` when calling my CSS Stylesheet?

WordPress recommends the proper way to enqueue the main style is the method-A. Please see the WordPress theme development handbook here (though both methods will work). https://developer.wordpress.org/themes/basics/including-css-javascript/

It’s not clear to me why you want to link the two .css file? You can create custom .css file and enqueue it using method-B.

However, if you want to import custom .css file to main style.css file you can use the CSS @import method. The syntex is as follows:

@import url(“../theme-name/css/bootstrap.css”);