Although old, this article is a good starting point: osxbook.com/book/bonus/ancient/whatismacosx/arch_…
Obviously, Apple has "customized" the system per their needs, but they share a lot of similarities with BSD type systems.
Binaries or applications are packages to OS X. Right click on an app and left click Show Package Contents and you'll see a bunch of files (depending on the app). An app can reside anywhere, though the preferred place is in the Applications folder.
You'll find very similar configuration files behind many OS X systems such as networking, sound, video, etc...
The broadness of your question makes it difficult to explain anything specifically, so pick a topic and learn 1 piece at a time.