What is the difference between publishing with an FTP program and doing it with Trellix alone?
Very little. In both cases your online files are being updated using the FTP protocol. The only significant difference is that when you completely delete or rename a file in your off line folder Trellix would automatically delete the online counterpart the next time you published. This, you will now need to do yourself, on occasion. Otherwise, the old undeleted online files will simply take up space that you may need later as you continue to add more content (files) to your web site.