Running multiple instances of CycleCloud on the same machine is supported, but requires some slight modifications to the configuration files before starting CycleCloud for the first time. During the install step, make sure to use the --nostart flag to keep the server from starting, and the --installdir flag to specify an alternate install directory. For example:
./install.sh --nostart --installdir /mnt/second_cycle_server
After the installer finishes, edit $CS_HOME/config/cycle_server.properties and change the following port numbers to an unused port (incrementing each default port number by one usually works well):
commandPort=6400 webServerPort=8080 webServerSslPort=8443 tomcat.shutdownPort=8007 brokerPort=5672 brokerJmxPort=9099 url=jdbc:derby://localhost:1527/cycle_server
Next, edit $CS_HOME/data/derby.properties and modify derby.drda.portNumber so that it matches the port specified in the url= line of cycle_server.properties.
Finally, copy /etc/init.d/cycle_server to a new file and edit the CS_HOME path to point to the new CycleServer install. Then start CycleServer using the new init script.