It sounds like you have built the pre-release from source, which is not required on the Pi and probably best recommended only for advanced users since the code in the flotilla-daemon-vs repo is rather cutting edge.
The easiest is to use the 'launch_flotilla' script provided at:
http://github.com/pimoroni/flotilla-pre
Alternatively you can overwrite /usr/bin/flotilla and /opt/rockpool/ in place on your system though I'd only recommend doing that if you are fluent with linux/raspbian.
