This is VERY high level, simply a reminder to myself and something for me to refer to.  But I'm also hoping that it is helpful to those needing to deciding what to do in these situations and to point them in the right direction.

1. If you already have mysql installed locally on your system, and you are installing wre, and you want webgui to use the system-installed mysql instead of the wre's mysql, you can adjust the wre.conf file to point to the system's mysql,  (create your databases, import your webgui data into the system's local mysql, test, and just never start up wre's mysql ever again)
   
   You can comment out the "all" and "mysql" options in the wreservice.pl script, to prevent you from starting it up by accident.
2. If you have other software using mysql and you are installing wre. and you want to have those other applications use wre's mysql, then adjust the configuration for those apps, to look at wre's mysql instance. (create your databases, import the data, test, and uninstall the system's mysql)
   
3. If you want to have multiple instances of mysql, then you would need to make sure each instance of MySQL bound to different TCP ports or to different (local) IP addresses if you have multiple IPs/interfcaes on your server.

If you are going to use a database other than wre's, then wreconsole.pl is not going to work. You'll need to either use addsite.pl at the command line, or create the database manually. You'll need to use the dbuser and dbpassword as specified in the sites's /data/webgui/etc/*.conf file.