The comment by @s29 should be an answer:
One way to add a directory to the virtual environment is to install virtualenvwrapper (which is useful for many things) and then do
mkvirtualenv myenv
workon myenv
add2virtualenv . #for current directory
add2virtualenv ~/my/path
If you want to remove these path edit the file myenvhomedir/lib/python2.7/site-packages/_virtualenv_path_extensions.pth
Documentation on virtualenvwrapper can be found at http://virtualenvwrapper.readthedocs.org/en/latest/
Specific documentation on this feature can be found at http://virtualenvwrapper.readthedocs.org/en/latest/command_ref.html?highlight=add2virtualenv