C:\Windows\System32\inetsrv\config\applicationHost.config

<system.applicationHost>
   <sites>
      <siteDefaults>
         <logFile logFormat="W3C"
            directory="%SystemDrive%\inetpub\logs\LogFiles"
            enabled="true">
            <customFields>
               <clear/>
               <add logFieldName="ContosoField" sourceName="ContosoSource"
                  sourceType="ServerVariable" />
            </customFields>
         </logFile>
      </siteDefaults>
   </sites>
</system.applicationHost>

appcmd.exe set config -section:system.applicationHost/sites /siteDefaults.logFile.enabled:"True" /commit:apphost
appcmd.exe set config -section:system.applicationHost/sites /siteDefaults.logFile.logFormat:"W3C" /commit:apphost
appcmd.exe set config -section:system.applicationHost/sites /siteDefaults.logFile.directory:"%SystemDrive%\inetpub\logs\LogFiles" /commit:apphost

using System;
using System.Text;
using Microsoft.Web.Administration;

internal static class Sample
{
   private static void Main()
   {
      using (ServerManager serverManager = new ServerManager())
      {
         Configuration config = serverManager.GetApplicationHostConfiguration();
         ConfigurationSection sitesSection = config.GetSection("system.applicationHost/sites");
         ConfigurationElement siteDefaultsElement = sitesSection.GetChildElement("siteDefaults");

         ConfigurationElement logFileElement = siteDefaultsElement.GetChildElement("logFile");
         logFileElement["logFormat"] = @"W3C";
         logFileElement["directory"] = @"%SystemDrive%\inetpub\logs\LogFiles";
         logFileElement["enabled"] = true;

         serverManager.CommitChanges();
      }
   }
}

var adminManager = new ActiveXObject('Microsoft.ApplicationHost.WritableAdminManager');
adminManager.CommitPath = "MACHINE/WEBROOT/APPHOST";
var sitesSection = adminManager.GetAdminSection("system.applicationHost/sites", "MACHINE/WEBROOT/APPHOST");
var siteDefaultsElement = sitesSection.ChildElements.Item("siteDefaults");

var logFileElement = siteDefaultsElement.ChildElements.Item("logFile");
logFileElement.Properties.Item("logFormat").Value = "W3C";
logFileElement.Properties.Item("directory").Value = "%SystemDrive%\\inetpub\\logs\\LogFiles";
logFileElement.Properties.Item("enabled").Value = true;

adminManager.CommitChanges();

<system.ftpServer>
   <log centralLogFileMode="Central">
      <centralLogFile enabled="true" />
   </log>
</system.ftpServer>

appcmd.exe set config -section:system.ftpServer/log /centralLogFileMode:"Central" /commit:apphost

appcmd.exe set config -section:system.ftpServer/log /centralLogFile.enabled:"True" /commit:apphost

using System;
using System.Text;
using Microsoft.Web.Administration;

internal static class Sample
{
   private static void Main()
   {
      using (ServerManager serverManager = new ServerManager())
      {
         Configuration config = serverManager.GetApplicationHostConfiguration();

         ConfigurationSection logSection = config.GetSection("system.ftpServer/log");
         logSection["centralLogFileMode"] = @"Central";

         ConfigurationElement centralLogFileElement = logSection.GetChildElement("centralLogFile");
         centralLogFileElement["enabled"] = true;

         serverManager.CommitChanges();
      }
   }
}

var adminManager = new ActiveXObject('Microsoft.ApplicationHost.WritableAdminManager');
adminManager.CommitPath = "MACHINE/WEBROOT/APPHOST";

var logSection = adminManager.GetAdminSection("system.ftpServer/log", "MACHINE/WEBROOT/APPHOST");
logSection.Properties.Item("centralLogFileMode").Value = "Central";

var centralLogFileElement = logSection.ChildElements.Item("centralLogFile");
centralLogFileElement.Properties.Item("enabled").Value = true;

adminManager.CommitChanges();