You can configure advanced options in the Site Manager for each site.
To edit a site's advanced options
Open the Site Manger (File > Site Manager).
In the left pane, click the site to be edited, then click Edit.
Modify the Site Properties for the particular site, then click OK.
Remote folder - Specify a default folder on the remote server that CuteFTP should navigate to as soon as you connect.
Local folder - Specify a default local folder on your hard drive that CuteFTP should navigate to as soon as you connect.
Account - Supply an account name (or keyword) for servers that require the ACCT command for logging in, post login, or for access to certain folders.
Transfer Type - Specify whether files should be transferred in ASCII, binary, Mac binary or if CuteFTP should auto-detect the correct transfer mode, or use the mode specified under Global Preferences.
Specify whether CuteFTP should use PORT or PASV mode when establishing the data connection with the server. PASV mode is the preferred method and the default one used when you use Global Preferences.
File name encoding - Specify standard encoding (ISO 8859-1), Unicode, or Double-byte encoding for international character support in CuteFTP Mac.
Use Proxy (firewall) server - Specify whether CuteFTP Mac should use your system proxy settings to negotiate a connection past your firewall (if applicable). You will have to specify the proxy host address when requested by CuteFTP Mac. You can obtain this information from your system administrator.
Set as default login site - Specify whether CuteFTP Mac should automatically connect to this site upon session startup.
Show hidden files and folders - Specify whether CuteFTP Mac should display "hidden" files or folders beginning with a period (such as .htacces).
Convert %NN in filename to the representative character - Specify whether CuteFTP Mac should use character sequences such as %20 to its representative character. (e.g., %20 is the same as a space.)
Keep connection alive sending NOOP command every N seconds - Specify whether CuteFTP Mac should attempt to keep a connection active by sending a NOOP (no operation) command every few seconds.
Set file upload permissions mask to NNN - Automatically apply a defined CHMOD sequence to a transferred item.