2 projects started already to create a GUI for this patched NotifyOSD. I tried compiling them and only one worked so I'm going to tell you how to compile / use it (it's very easy).
Before installing the graphical user interface to customize NotifyOSD, firstly make sure you add the PPA with the patched NotifyOSD (see here).
bzr branch lp:notifyconf
cd notifyconf/
make
sudo make install
Then to run it, type this in a terminal (there's no menu entry just yet):
notifyconf
Update: there is now a PPA available For NotifyOSD Configure GUI
The GUI isn't perfect (
Besides allowing you to configure NotifyOSD notification bubbles, NotifyOSD Configuration also creates a preview of your settings once you click the "Apply" button and you can save and load themes (so people can already start creating themes!).
And this is not the only GUI for configuring NotifyOSD. Another one can be found HERE. Hopefully they will also get a Launchpad PPA for easier installation (if not, I may do it if I have some time).