You can change the default directory for notebooks. It can be done permanently in ipython notebook config files. Firstly, locate the ipython profile, in the cmdline, type:
$> ipython locate
Default profile location (using Anaconda) is: %USERNAME%\.ipython
then, in file ipython_notebook_config.py
(if it's default profile go into folder \profile_default), uncommnet and edit line:
c.FileNotebookManager.notebook_dir = u'C:\\Users\\Lukasz\\Documents\\Github'
changing the my path to whatever path you like.
Really useful website is: http://ipython.org/ipython-doc/dev/config/intro.html
After above step Ipython should start with proper path.
It works for me.