I can see you are trying to write your own MVC so I will try to explain things you should be aware of while doing this.
First thing you want to do while writing MVC is utilize Front Controller pattern.
What this means is that every HTTP Request will go through one file, index.php.
This will help you to cofigure your application in one file. You can do this by just always opening your lets say:
www.example.com/index.php/controller/method/param1/param2
or you can force users to go through index.php using .htaccess file.
For reference check other frameworks like Codeigniter and CakePHP, see how they use .htaccess files.
When you are in your front controller file, you should think about routing your HTTP Request to appropriate Controller / Method. There are really lots of ways to achive that, and its up to you to figure out the best way to do that.
Anyway you need Router class that will analyse your URL, and extract Controller / Method / Params you need from URL. Then when you know what Controller / Method you need to invoke, you need Dispatcher class that would instantiate Controller, and call Method you need. You should also think about Params you want to pass to your Method so you can use them there.
The easiest way to play around with this is to use query strings.
So lets say you have URL like this:
http://localhost/test/index.php?controller=home&method=welcome
You can easily get Controller and Method names.
Now you can do something like this:
// Get controller and method names
$controller = $_GET['controller'];
$method = $_GET['method'];
// Instantiate controller object
$app = new $controller();
// Call method on you controller object
call_user_func_array(array($app, $method));
This is like the simplest thing you can do just to play around.
Once you get hold of this, write your Router class so it can look like this:
http://localhost/test/index.php/controller/method/param1/param2
Anyway you need these classes:
Front Controller so every request goes through one file, and this is where you bootstrap you application, register class autoloading, configure everything etc...
This is not a class but a file with procedural code that boots everything up.
Router that will analyse URL and give you back Controller, Method, and Params that you want to pass to invoked Method.
Dispatcher that will instantiate Controller and call Method passing Params to your Method.
And then all control goes to user of your system, then you do your magic inside your controller / method.
While Dispatching request you can also use this:
call_user_func_array(array($app, $method), $params);
this way you are passing $params to $method, so you can use $params inside your method.
Also, check out Reflection class, this can help you to analyse if method you want to invoke exists, if not you should call HTTP 404 etc...
There is no simple answere to your question, but I hope this helps,
have fun building your system and just improve until you get it perfect :)