The file system is simple---once you understand it...
It it is one tree starting with "/" which is often called "root". Type "cd /" and then "ls", and you will see the directories in the top level of the tree. You can then "cd" into each one to see the contents.
Here is a very crude partial list of what goes where:
/bin system programs normally needed by users
/sbin system programs normally used by administrators
the distinction between these 2 is not always crisp
/lib library routines called by other programs
/etc configuration files (for all users)
/usr things installed by and for users. A lot of applications go here
/opt optional stuff---applications often go here also
/home directories associated with specific users (configuration files--eg e-mail--will be in /home/username--often as hidden files.
While the convention says that you would put applications in /bin , /sbin , /usr/xxx, or /opt/xxx, the fact is that you can put an application just about anywhere you want. Configuration files, however, have to be where the program expects to find them.
Personal files normally go in /home/username. Again, you can put them whereever you want.
Linux---like Unix---is at its core a general purpose, multi-user, system. In a typical installation, you might never use many of the subdirectories.