I think your answer might still not be answered completely.
You mention you have managed to successfully use tar, but I am not sure you have actually managed to install software nonetheless. (You dont need to copy any file anywhere. The installation is completely automated in most cases, all you need to do is enter three commands.)
Just to make sure, have a look at this article about compiling (and installing) software from source in linux
It is really not necessary to have an in-depth understanding of the file system to use a linux system. However, if you feel more comfortable knowing about it, look at this description
Making links to programs does not require you to know where the binaries are either. Any command you can run from the command line can also be executed from within the desktop environment. If you still want to find out where the binary is located, try using the command which
). Use the man pages (e.g.: man which
Good luck with linux,