Extending xml rpc – best practice

If I have lots of custom methods what
is the best approach to handling this?

Instead of filtering xmlrpc_methods, you could extend the wp_xmlrpc_server class and set your class as default with the filter wp_xmlrpc_server_class.

// Webeo_XMLRPC.php
include_once(ABSPATH . WPINC . '/class-IXR.php');
include_once(ABSPATH . WPINC . '/class-wp-xmlrpc-server.php');

class Webeo_XMLRPC extends wp_xmlrpc_server {
    public function __construct() {
        parent::__construct();

        $methods = array(
            'webeo.getPost' => 'this:webeo_getPost',
            'webeo.getPosts' => 'this:webeo_getPosts'
        );

        $this->methods = array_merge($this->methods, $methods);
    }

    public static function webeo_getName() {
        return __CLASS__;
    }

    public function sayHello($args) {
        return 'Hello Commander!';
    }

    public function webeo_getPost($args) {
        // do the magic
    }

    public function webeo_getPosts($args) {
        // do the magic
    }
}

add_filter('wp_xmlrpc_server_class', array('Webeo_XMLRPC', 'webeo_getName'));