HBB loaded and running; how to add additional HomeBridge?

Starting from a clean environment, I have used Homebridge Buddy to install and run Homebridge and have it working with Apple HomeKit.

It is probably in the docs somewhere, but haven't been able to sort out (and probably getting a little confused between HBB and Webdeck Indigo plug-in):

How do I install/configure additional HomeBridge servers? My understanding is that if I want to load additional HomeBridge plug-ins such as for cameras, Nest thermostat, or other devices I am supposed to create a separate HomeBridge for that and not interfere with the HomeBridge that is automatically created and controlled by HBB. Would this be done "behind the back / outside" of HBB completely, or would the HBB plug-in handle creating the additional HomeBridge servers and be able to start/stop them?

For the HomeBridge server created by HBB, where are the HomeBridge and/or other actual configuration files stored? I may want to manually edit/change the configuration or archive them to make it easier to experiment and then "rollback" to a known good configuration. (Or maybe I need to be pointed to the recommended way to deal with this.)

The HBB configuration places all my Indigo devices into HomeKit's "default room". It is tedious to move these around to different rooms and then have to repeat all this re-configuration if I reconfigure/re-install everything.

Thanks!

P.S. - It is really awesome the way HBB has automated installing node.js and creating/running HomeBridge automatically. Is there any "behind the curtain" overview of how this is all done from inside an Indigo plug-in? Looks like magic to me.

Secret sauce for the embedded homebridge: https://github.com/webdeck/homebridge-indigo-packager