There are limitations as to how the daemon can be setup in different configurations. The basic principle is one daemon per database and it can be summarized like this:

• One server - one eZ Publish installation - one database - one daemon: In this configuration there should be one daemon monitoring one publishing queue. 
• One server - separate eZ Publish installations - separate databases - one daemon per database: In this configuration there should be one daemon per database. Each daemon is started by a separate script in /etc/init.d/ 
• Several servers - one eZ Publish installation - one database - one daemon: In a clustered configuration there can only be one daemon set up on one of the servers. One publishing queue, one daemon.