My python program consists of several files: 

the main execution python script
python modules in *.py files
config file
log files
executables scripts of other languages.

All this files should be available only for root. The main script should run on startup, e.g. via upstart.
Where I should put all this files in Linux filesystem? 
What's the better way for distribution my program? pip, easy_install, deb, ...? I haven't worked with any of these tool, so I want something easy for me.
The minimum supported Linux distributive should be Ubuntu.
If only root should access the scripts, why not put it in /root/ ?
Secondly, if you're going to distribute your application you'll probably need easy_install or something similar, otherwise just tar.gz the stuff if only a few people will access it?
It all depends on your scale..
Pyglet, wxPython and similar have a hughe userbase.. same for BeautifulSoup but they still tar.gz the stuff and you just use setuptools to deply it (whcih, is another option).
Where I should put my python scripts in Linux?