There is some kind of "Filesystem Hierarchy Standard":
The Filesystem Hierarchy Standard (FHS) defines the main directories
and their contents in Linux operating systems. For the most part, it
is a formalization and extension of the traditional BSD filesystem
hierarchy.
I would put that stuff to:
/opt/ Optional application software packages
Read yourself: http://en.wikipedia.org/wiki/Filesystem_Hierarchy_Standard
For the rest of your questions:
That's a matter of having the path to the binary / script you want to launch in the PATH variable. According to https://help.ubuntu.com/community/EnvironmentVariables you want to do this via /etc/environment. You could also create a 'symbolic link' to the binary or write a launch script which you then place into /usr/bin or /usr/local/bin.
See 1.
For that you have to create a .desktop file and install it (make an entry in the menu to it) via xdg-desktop-menu.