Generally i would not recommend you to create your own framework, but if you insist or want to do it for learning purposes the PHP community created FIG (Framework Interop Group) to maintain consistency between frameworks, and how things should be handled.
The problem you are trying to solve is called autoloading, it's also documented AS PSR-0 standard, https://github.com/php-fig/fig-standards/blob/master/accepted/PSR-0.md, Have a nice read.
And here is PSR-0 compliant autoloader examples: PHP - most lightweight psr-0 compliant autoloader
Basically it means that your namescape path will tell where to look for file.
For example you want to get BussinessObject in bootstrap.php:
//MVC/Models/BussinessObject.php
namespace MVC/Models;
class BussinessObject {
}
//MVC/bootstrap.php
namespace MVC;
use MVC/Models/BussinessObject;
$BussinessObject = new BussinessObject()
Then autoloader will look for file in MVC/Models/BussinessObject.php, and calls require using that path.