Entities passing them or using a class

I am new to coding so I do not know if I have this concept correct? Suppose I create a custom entity then extend it and add properties to the class are my added properties similar to properties like nid and title? If that answer is yes, I assume one would create properties rather than fields on the entity class to do custom logic?

What I have been doing is creating Content Type Bundles Querying them in a Form using Dependency Injection then parsing through the form_state the new updated nodes. In other words I am passing the objects in a foreach to update the fields. Should I be adding properties to a class and have those update? Or a combination?