Enque a stylesheet in functions.php to override Bootstrap

Note

wp_enqueue_style()

should be placed inside a callback function to wp_enqueue_scripts

add_action( 'wp_enqueue_scripts', 'callback' );

Like your code in the question shows, so put your loading of the custom stylesheet with wp_enqueue_style() inside it.

Last but not least, CSS is processed in a way that the last style definition is used. So by loading your stylesheet after the default one you can override the default definition with your custom one. The definitions, the element targeting, must be equal to make this work.