When configuring my Security system does it matter where I do some or most of the configurations? What I am asking is, does the configuration on the cameras web interface like bit rate, frames per second, etc take precedence over Blue Iris or vice versa?
Blue Iris does not allow you to set bitrate, FPS, etc. for the camera Blue Iris is a recording and management program and records based on what is fed to it from the camera.
You set up anything that can be setup in the camera GUI.
You can use motion detection from the camera and pull in via ONVIF triggers or use BI motion triggers.