ok,I think you need a nice book, or some useful links
and so on.
Redhat Based Distro like CentOs uses rpm Packages for installation.
command to learn: rpm
Then there are files with install scripts an so on, described in makefile's tar.gz, bz2, stuff like
that. Most of those applications bring a README along, with command switches.
FHS = Filesystem Hierarchy System (should be most standard on nearly all Linux Distros)
/opt = install place for optional software
/srv = additional services
/tmp = temp.files
/var = common place for variable files like log-file from apache and so on
/lib = libraries that are used by services, programs, and so on
/usr = UNIX System Resources
/home = standard folder for homedirectories if a user is added with useradd or adduser command (most common)
The question you've got is very huge so not easy to answer in a single post.
I hope that someone else in this forum will post some good LINKS.