Hello Lewis,
The console option is under Windows only. If you are starting Linux AC3D from a terminal window, any script output (tcl 'puts') will go there. It will be purely used for output.
You can add your own scripts in the scripts folder - they will be run when AC3D starts up.
It is possible to connect to AC3D via a socket and control AC3D (this can even be done remotely) . Once the socket is enabled (advanced settings), you can use telnet (or similar) to connect to AC3D and control it.
Andy