Use N/config to load the general preferences record and set it and save the record.

Please follow the below code snippet:

/**
 * companyPreferences.js
 * @NApiVersion 2.x
 * @NModuleScope Public
 */
//Sample Config load and get Value or set Value
define(['N/config'],
    function (config) {
    //Please visit config module for types in help
        function loadCompanyPreferences() {
            const shopifyApi = config.load({
                type: config.Type.COMPANY_PREFERENCES //depends on your requirement
            });
            const apiKey = shopifyApi.getValue('field ID');
            shopifyApi.setValue('field ID', 'value');
            shopifyApi.save(); //You can use the ignore or field sourcing
        }

        return {
            compPref: loadCompanyPreferences
        }

    });