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.

Nothing to add to @mgiambanco's response other than the best way to really learn whats under the hood is to use it. Best way to do that is to use Terminal for things that you might not do otherwise. For example, use ifconfig to look up your ip address rather than network utility, or using mount to see what file systems you have mounted. The more you use it, the more you will understand how things fit together.

Note that there's a difference between "apps" (those that live in /Applications or ~/Applications and programs such as ifconfig etc that live in /sbin. Apps are just packages with programs and other files inside them. You can see where any given program is located by using which in your Terminal. For example, to see where ifconfig lives, just type which ifconfig.

Finally, apropos and man are your friends in Terminal. The first will return a list of results from the documentation that is available on your machine for a given command, and the second gives you access to the documentation itself. For example, if you type apropos ifconfig you'll see there's only 1 match, or apropos git and you'll see there are lots. Typing man ifconfig will give you the documentation for that command. Hit Q to quit apropos or man, or space to go to the next page of results when there are lots.