There are two ways to get files onto your server: SSH and SFTP. We recommend SFTP instead of SSH for its ease of use.
SFTP is a secure form of FTP (file transfer protocol) that runs over SSH on port 22.
Several SFTP clients exist, but we like Cyberduck for its clean interface and simple drag-and-drop-ability.
Also, Cyberduck is free and runs on both Windows and Mac OS X systems. Both versions can be downloaded at https://cyberduck.io.
For more on setting up an SFTP client, check out our tutorials on installing Cyberduck and uploading files.