It is not usually necessary to use a CMS such as Drupal and Joomla with the Premium Website Builder. If you are looking to build a site that needs more functionality than the builder offers, I would suggest simply using a CMS for the entire site instead.
It's hard to say what tool would work best for you without more information. Can you please expand on your description of "ecommerce and FTP sites?" Feel free to either update your question or add a comment below with more information.
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