The Tools menu gives you access to several additional features of the application, including Quick Synchronize, Public Key Creator, Public-Key Assistant, etc.
In the File Transfer Options tab you can modify various transfer options, including the number of connection attempts, the delay between attempts and others.
The Advanced File Transfer Options tab allows you to enable some features like 'Move deleted local files to the Recycle Bin', '
Keep connections alive' or 'Never use cached file for remote editing'.