Could you repeat the question?----
Seriously, short posts with very specific questions are better.
Filesystem: Ancient customs date back to early days of Unix--built around the concept of many users and central administration. Here
is one link that may help.
Compiling: first, you don't need to do this unless you cannot find something in you repository--or find an .rpm file. (make, configure, etc. all have to do with compiling) See below on installing SW...
Especially when starting out, use the repositories first. Second choice is to get an .rpm file and install at the command-line. The LAST choice is compiling from source. Using anything but the repositories carries the risk that you will have to hunt down some "dependencies"--our scary word for libraries that are needed for a particular application. The package manager spares you this trauma.
Final wisdom--which few of us follow: One step at a time.