Kind of a tough question there gary. I'm not sure I completely understand all that you are asking, but let me see if I can explain in a simple way about files on your PC.
A fair analogy would be, "
my house has a lot of wires"....

You may not be able to see each wire or know its specific purpose, but you know they are all connected to various outlets or appliances in the house. So it should be the appliances or outlets you are looking to use, not necessarily the wires.
Same thing with the PC. There are many files. You may not be able to open, or use individually every single file on your PC, but various programs will use them to preform different tasks. Some programs use a large number of files to preform tasks, and others maybe only a select few. But like the appliances in your house, its the Programs you are looking to make use of. In turn, each program will make use of the various files. So don't think of it as needing to see each and every file.
Now having said all this, lets talk about important individual files. Documents for example. You would use something like Microsoft Word to create, edit and save a document file. The program, Microsoft word might make use of 50 various files on your PC without you ever knowing it, to preform the changes you make to your document . But the end result is your single document having been created, and edited just the way you want it. Same thing with images. A program like Adobe Photoshop will use hundreds of files to operate and do all the various things you would need, to manipulate, view, and edit, a picture file. The final product is the image file you changed or edited. But it takes all those other files to create or edit your one image.
I hope I am making some sense here....its been a long night at work...lol Anyhoo....Hopefully this helps a little.
Grace and Peace!