1.) Factory settings
The factory settings are hardcoded fallback settings.
2.) Configuration file Krexx.ini
The configuration file settings are stored in the file Krexx.ini. kreXX shows in it's output footer where it is searching for this file. In typo3 this is normally:
uploads/tx_includekrexx/Krexx.ini
3.) Local browser settings
You can edit the local browser settings on the fly in the footer of the kreXX output. They are stored in a cookie, and only affect your current browser. Unlike the configuration file, not all settings can be edited there.
Local browser settings overwrite configuration file settings.
Please note, that these are only local settings, only affecting your current browser.