Windows Live Writer is configured for working with WordPress multi-site the same way as with normal single-site WordPress installation, but WordPress works a bit differently in multi-site and single-site configurations. The difference consists in a few lines of code in wp-includes/class-wp-xmlrpc-server.php:
function wp_getUsersBlogs( $args ) { global $current_site; // If this isn't on WPMU then just use blogger_getUsersBlogs if ( !is_multisite() ) { array_unshift( $args, 1 ); return $this->blogger_getUsersBlogs( $args ); } //single-site verion... }