A user's ChimeraX preferences are stored along with the command history and file history in a standard platform-dependent location (for example, ~/Library/Applications/ChimeraX and subdirectories on a Mac; see python appdirs).
Choosing UCSF ChimeraX... Preferences from the menu shows the main Preferences dialog, with sections:
Save saves the current settings, Reset replaces the current settings with the initial (“factory”) defaults, and Restore replaces the current settings with those previously saved; if the Buttons affect all categories option is checked, these buttons apply to all sections of the Preferences dialog, not just the section currently shown.
Model number will be included when multiple models are present.
Some preferences do not apear in the dialog, but can be adjusted and saved by other means: