This snippet will edit/add a number of settings to modx_system_settings.

pepebe_updateSystemSettings.snippet.php

<?php
/*
 * This snippet will edit/add a number of settings to modx_system_settings.
 * The $settings array MUST contain all relevant information. 
 * Use the example below to create your own list of relevant settings.
 * 
 * Updating settings
 * -----------------
 * All settings allready present in the database are updated by this script.
 * Keep in mind to send the correct type of data. So don't add "hello" to a key with xtype "combo-bolean".
 *
 * Adding new settings
 * -------------------
 * If a setting is not present, the snippet will add it to the database. 
 * Keep in mind, that if you don't specify the correct properties, modx will set standard properties for you
 * 
 * Available properties:
 * - value      - mandatory - default: empty
 * - namespace  - optional  - default: "core"
 * - area       - optional  - default: "default"
 * - xtype      - optional  - default: "textfield"
 *
 * Available xtypes:
 * - combo-bolean
 * - modx-combo-bolean
 * - numberfield
 * - text-password
 * - textarea
 * - textfield
 *
 * */

$debug = false;

$msg['snippet'] = 'pepebe_updateSystemSettings';
$msg['debug'] = $debug;

$settings = array(
    /* personal settings */
     'pepebe.bootstrap.path' => array(
         'value'        => 'assets/libs/bootstrap/3.3.7/'
        ,'namespace'    => 'pepebe'
        ,'area'         => 'libs'
        ,'xtype'        => 'textfield'
    )
    ,'pepebe.isotope.path' => array(
         'value'        => 'assets/libs/isotope/3.0.2/'
        ,'namespace'    => 'pepebe'
        ,'area'         => 'libs'
        ,'xtype'        => 'textfield'
    )    
    ,'pepebe.jquery.path' => array(
         'value'        => 'assets/libs/jquery/1.12.4/'
        ,'namespace'    => 'pepebe'
        ,'area'         => 'libs'
        ,'xtype'        => 'textfield'
    )
    ,'pepebe.lightbox2.path' => array(
         'value'        => 'assets/libs/lightbox2/2.9.0/'
        ,'namespace'    => 'pepebe'
        ,'area'         => 'libs'
        ,'xtype'        => 'textfield'
    )
    /* modx default settings */
    ,'friendly_alias_translit' => array(
         'value'        => 'german'
    )
    ,'manager_time_format' => array(
         'value'        => 'H:i'
    )
    ,'manager_date_format' => array(
         'value'        => 'd.m.Y'
    )
    ,'date_timezone' => array(
         'value'        => 'Europe/Berlin'
    )
    ,'locale' => array(
         'value'        => 'de_DE.UTF-8'
    )
    ,'cultureKey' => array(
         'value'        => 'de'
    )
    ,'friendly_alias_restrict_chars_pattern' => array(
         'value'        => '[^a-zA-Z0-9 _-]'
    )
    ,'fe_editor_lang' => array(
         'value'        => 'de'
    )
    ,'manager_lang_attribute' => array(
         'value'        => 'de'
    )
    ,'manager_language' => array(
         'value'        => 'de'
    )
    /* modx extras settings */
    ,'redactor.lang' => array(
         'value'        => 'de'
        ,'namespace'    => 'redactor'
        ,'area'         => 'Internationalisation'
        ,'xtype'        => 'textfield'
    )

    ,'collections.mgr_date_format' => array(
         'value'        => 'd.m.Y'
        ,'namespace'    => 'collections'
        ,'area'         => 'manager'
        ,'xtype'        => 'textfield'
    )
    ,'collections.mgr_time_format' => array(
         'value'     => 'H:i'
        ,'namespace'    => 'collections'
        ,'area'         => 'manager'
        ,'xtype'        => 'textfield'
    )
    ,'collections.mgr_datetime_format' => array(
         'value'        => 'd.m.Y H:i'
        ,'namespace'    => 'collections'
        ,'area'         => 'manager'
        ,'xtype'        => 'textfield'
    )    
);

$msg['elements'] = count($settings);

if (!$modx->hasPermission('settings')) return false;

if (!function_exists('pepebe_updateSystemSettings')) {
    /**
     * Sets the system settings
     * @param string|array $key
     * @return array|null|string
     */
    function pepebe_updateSystemSettings($settings,$debug)
    {
        global $modx;
        if (!empty($settings)) 
        {
            if (is_array($settings)) 
            {
                foreach ($settings as $key => $setting) 
                {
                    $changed++;
                    
                    $updateObject = $modx->getObject('modSystemSetting', $key);
                    
                    $msg[$key]['options'] = $setting;
                    
                    if(!empty($updateObject))
                    {
                        /* update setting */
                        $updated++;
                        
                        $msg[$key]['action']['type'] = 'update';
                        $msg[$key]['old_value'] = $updateObject->get('value');
                        $msg[$key]['new_value'] = $setting['value'];
                        
                        if(!$debug)
                        {
                            $msg[$key]['action']['result'] = 'setting changed';
                            
                            $updateObject->set('value', $setting['value']);
                            
                            $updateObject->save();
                        }    
                        else 
                        {
                            $msg[$key]['action']['result'] = 'setting not changed (debug mode)';
                        }
                        
                    }
                    else 
                    {
                        /* create setting */
                        $created++;
                        
                        $msg[$key]['action']['type'] = 'create';
                        $msg[$key]['old_value'] = "";
                        $msg[$key]['new_value'] = $setting['value'];
                        
                        if(!$debug)
                        {
                            $msg[$key]['action']['result'] = 'setting added to system settings';
                            
                            $createObject = $modx->newObject('modSystemSetting');
                            $createObject->set('key',$key);
                            $createObject->set('value',$setting['value']);
                            $createObject->set('namespace',$setting['namespace']);
                            $createObject->set('area',$setting['area']);
                            $createObject->set('xtype',$setting['xtype']);
                            $createObject->save();
                        }
                        else 
                        {
                            $msg[$key]['action']['result'] = 'setting not added (debug mode)';    
                        }
                        
                    }
                      
                    
                }
                $msg['status']['changed'] = $changed;
                $msg['status']['updated'] = $updated;
                $msg['status']['created'] = $created;
                
                return $msg;
            }
            else 
            {
                $msg['status'] = 'Error: settings must contain an array';
                return $msg;
            }
        } 
        else 
        {
            $msg['status'] = 'Error: settings cannot be empty';
            return $msg;
        }
    }
}

$msg['settings'] = pepebe_updateSystemSettings($settings,$debug);

/* reload the config or you'll just get the old version from the config cache */
$modx->reloadConfig();

/* get new values */

foreach($settings as $key => $value) {
    $msg['settings'][$key]['new_value'] = $modx->getOption($key);    
}


return "<br><pre>".print_r($msg,true)."</pre>";