[Mark Nord]

A,

Core.settings.saveOptions(yourNameHere);

simply saves all option-values not equal to default.

Code in spoiler taken from BookManagement.js

Spoiler:

optionDefs: [
			{
				name: 'subCollections',
				title: L('SUB_COLLECTIONS'),
				icon: 'BOOKS',
				defaultValue: 'false',
				values: ['true','false'],
				valueTitles: {
					'true': L('VALUE_TRUE'),
					'false': L('VALUE_FALSE')
				}
			},
			{
				name: 'subCollSeparator',
				title: L('SUB_COLLECTIONS_SEPARATOR'),
				icon: 'BOOKS',
				defaultValue: '|',
				values: ['|', '.', ',', ':', ';', '/', '~'],
			},
			{
				name: 'clearHistsOnShutdown',
				title: L('CLEAR_PAGE_HISTORY_ON_SHUTDOWN'),
				icon: 'CLOCK',
				helpText: L('CLEAR_PAGE_HIST_HELPTEXT'),
				defaultValue: 'false',
				values: ['true', 'false'],
				valueTitles: {
					'true': L('VALUE_TRUE'),
					'false': L('VALUE_FALSE')
				}	
			}
		],

Again, without knowing your code it is hard to be more specific.