Did you configure Soundflower to map its outputs to your internal soundcard? Soundflower is a virtual audio device that you can use in between an audio application and any other audio device. You however need to setup the right mappings in Soundflower bed that comes with the software. You also need to select the right audio device in EigenD by going to the Window -> Audio Settings menu in EigenD.
On another note though, you're note required to use Soundflower with EigenD, only do so if you have a good reason for it since it introduces additional latency from Soundflower itself.
Hope this helps,
Geert