It is not possible to save new default values for configuration options in JuiceboxBuilder-Pro but you can save a custom combination of configuration options as a 'Preset' file ('Presets -> Save Preset...' from the drop down menu at the top).

When you next edit or create a gallery, you can apply this 'Preset' file to your gallery (to set all your custom configuration options at once and save you from having to set them all individually) via 'Presets -> Load Preset...'.

You can have as many 'Preset' files as you like (each holding different configuration option values).
Please see the 'Presets' section of the JuiceboxBuilder-Pro User Guide for more information.

(You can save new default values only for image sizes. On the 'Images' tab, you can click the 'Change Sizes...' button in the 'Image Size' control panel to set image dimensions and, if you click 'Save Defaults', then the current values will become default values for new galleries.)