If you have a website built using a database such as Wordpress, Joomla, Drupal, osCommerce or any other script, it is best to use SEIntelligence's download from URL option.
Because these websites are dynamic, you won't want to re-upload the site again. It is best to apply the recommendations using the content management system's backend features.
Tip: When downloading a dynamic website in SEIntelligence, got the Preferences window (under the SEIntelligence menu) and select 'Download Websites'. From there you can restrict certain pages from being downloaded which will result in faster downloads.