The IPython documentation pages suggest that opening several different sessions of IPython notebook is the only way to interact with saved notebooks in different directories
The interface and architecture design issues for multiple directory support (and more generally for "project" support) for iPython notebook are important to get right. A design is described in
IPEP 16: Notebook multi directory dashboard and URL mapping
and is being discussed at IPEP 16: Notebook multi directory dashboard and URL mapping · Issue #3166 · ipython/ipython