In an attempt to add a bit of modability to my game, I want to make it so that all of the .cpp/.h files in a certain directory are included. Files are NOT my strong point, so I have absolutely NO idea as to how I will do this.
Files are not your strong point? I don't really know what this has to do with files and if you are programming your own game you should absolutely know how to do this. Programming a game engine OR working with a game engine is incredibly difficult so I would suggest learning (A LOT) more before getting involved in that.
Just so you know I'm not trying to put you down but rather help you in the long run. As far as your question, you need to go to your project properties and add the folder to your projects include list. I can't really give you a step by step tutorial as it varies from IDE to IDE.
Take a look at boost::filesystem. It will let you iterate through each file in a directory, check the extension, etc. I'm guessing that you'll need to write a program to build your project.
Otherwise, something that is standard practice is to build DLLs. This way, to change your game, you don't need to get the user to compile it. They simply place the DLL in the bin directory. The source-code for each DLL will remain known.