There are several secure file transfer protocols, SFTP and FTPS namely. When you are supposed to transfer files to some server, you need to use protocol that the server supports. Ask server administrator for that. Once you know the server, you can use WinSCP to connect and transfer the files.

See other guides for individual steps:

• Download and install WinSCP
• Connect to FTP/SFTP server
• Upload files to FTP/SFTP server