Conditionally print css style in WordPress

Use the function body_class() in your templates:

<body <?php body_class(); ?>>

This creates extra classes on the body element. Then filter its values in your functions.php:

add_filter( 'body_class', function( Array $classes ) {

    if ( $GLOBALS[ 'isBoxedLayout' ] )
        $classes[] = 'isBoxedLayout';

    return $classes;
});

Now you can move all CSS declarations for that to your stylesheet:

.isBoxedLayout #container {
    width:999px;
}