This allows you to get statistics about your web site. When you start CuteFTP the first time, it takes you through a survey and then runs the connection wizard for initial setup. At the end, you re asked if you want to make this your default connection upon startup. Once you re done with the wizard, site manager starts. This is a folder type layout grouping FTP sites by classification, but you could edit to get the listing however you like.
Site manager includes all the commands for managing the folders and adding sites.
To open a site, just double-click on it, or highlight and click connect. At the top is the log window that logs all commands, responses, errors, etc between the client and the remote site. The local window shows the directory listing on your machine. The remote window the directory listing on the remote server. These windows are much more explorer like than version 2.0 was.