There are numerous ways to structure the code and project for you web application, and you can put as much or as little thought as you like into architecting. But it is usually a good idea to follow to common patterns because it will make your code easier to manage and easier for others to understand.
One of the most commonly used design patterns is the factory pattern. In this pattern, a class simply creates the object you want to use. Consider the following example of the factory pattern:
This code uses a factory to create the Automobile object. There are two possible benefits to building your code this way, the first is that if you need to change, rename, or replace the Automobile class later on you can do so and you will only have to modify the code in the factory, instead of every place in your project that uses the Automobile class. The second possible benefit is that if creating the object is a complicated job you can do all of the work in the factory, instead of repeating it every time you want to create a new instance.
Using the factory pattern isn’t always necessary (or wise). The example code used here is so simple that a factory would simply be adding unneeded complexity. However if you are making a fairly large or complex project you may save yourself a lot of trouble down the road by using factories.
The front controller pattern is where you have a single entrance point for you web application (e.g. index.php) that handles all of the requests. This code is responsible for loading all of the dependencies, processing the request and sending the response to the browser. The front controller pattern can be beneficial because it encourages modular code and gives you a central place to hook in code that should be run for every request (such as input sanitization).
The model-view-controller (MVC) pattern and its relatives HMVC and MVVM let you break up code into logical objects that serve very specific purposes. Models serve as a data access layer where data it fetched and returned in formats usable throughout your application. Controllers handle the request, process the data returned from models and load views to send in the response. And views are display templates (markup, xml, etc) that are sent in the response to the web browser.
MVC is the most common architectural pattern used in the popular PHP frameworks.
Learn more about MVC and its relatives: