I've been having problems with Soundflower slowly going out of sync so had a look for an alternative.
I'm now using Rogue Amoeba's Audio Hijack Pro to directly capture the output from EigenHost without using a seperate audio rerouter like Soundflower (although note that AHP isn't free, but $32 seemed pretty low for what it does).
The thing I really like about it is that you can leave it recording *all the time*. It doesn't record silence, and automatically starts a new MP3 file when silence is detected. This is great for me because it means I don't have to remember to do anything to record. Both EigenD and AHP start on logon. After that, anything I play on the Pico is recorded automatically. If I stop playing for a bit then start again later on, it starts a new MP3.
Note that in Audio Hijack Pro the application you need to 'hijack' the audio from is 'EigenHost', and if you want EigenD and AHP to start up at login, you need to delay AHP by 30 seconds or so by using Automator.