ATHENA allows you to set an enormous number of preferences. Many dozens of things that could conceivably be configured can, in fact, be configured using this tool. In any situation where is was not obvious to me that there was a best, most proper value for a parameter, I chose a default and made an entry for it in the preference tool. The preference tool is shown here.
I am not going to explain this tool in great detail. I am trusting that if you are sufficiently motivated to configure the behavior of ATHENA to be something other than what comes out of the box, you will also be sufficiently motivated to follow your nose through the use of this tool.
The preference parameters are divided into related groups. For example, there are groups for background removal parameters, alignment parameters, colors, and so on.
To view a group of preferences, click on the little cross sign next to the group's name in the list on the left side of the tool. This will open a branch containing all the parameters in tat group. Click on one of them and it will be displayed in the controls on the left.
Click on the default button to restore ATHENA's default value or use the control below the default button to set a new value. That control will vary depending on the type of parameter. A text or numeric parameter will offer an entry box. A color parameter will offer a button which pops up a color selection dialog. A list parameter will offer a menu with the choices. And so on.
The text area below these controls displays an explanation of the function served by that preference. Underneath that are buttons for setting or saving the parameters.
Various configuration files, including the master configuration file demeter.ini and others, are stored in user space. On linux (and other unixes) this is $HOME/.horae/. On Windows this is %APPDATA%\demeter.