There are a handful of ways to upload files to WSO. Option 1, of course, is the command line. From a Unix command line, typing "scp [file or folder to upload] [your user name]@wso.williams.edu:[path to upload to] will do the trick. "scp" is short for secure copy. When you use scp, all of your data is encrypted before being transferred to WSO.
You can also upload files to WSO via the Secure File Transfer Protocol (or SFTP for short). SFTP is just like regular FTP except that it encrypts all data before forwarding it along. From a Unix command line, you can launch an interactive SFTP session by typing "sftp [your user name]@wso.williams.edu". Once you're connected, you'll be able to navigate around your local machine and the WSO server using variants of the standard Unix commands (i.e. use cd to change directories on the remote machine, lcd to change directories on your local machine, ls to list the contents of a remote directory, lls to list the contents of a local directory, etc). Typing "help" will get you a complete list of recognized sftp commands (along with descriptions).
For the more graphically minded, there are lots of free SFTP GUI applications. WinSCP is a free SFTP client for Windows that can be downloaded from http://winscp.net/eng/index.php. Fugu is a free SFTP client for Mac OS X that can be downloaded http://rsug.itd.umich.edu/software/fugu/. Once you have an SFTP client installed, use it to open a secure connection to "wso.williams.edu". Most SFTP clients have a two panel inteface. The left panel represents your local computer and the right panel is the remote machine. Find the file you want to backup in the left panel and drag it to where you want to store it on the right panel. You can do this for multiple files at once by highlighting more than one file in the left panel.
A second popular SFTP application for Mac OS X is Cyberduck, which is available as a free download from http://www.apple.com/downloads/macosx/internet_utilities/cyberduck.html. Cyberduck supports a single panel interface that might be appealing to some users. It also supports a variety of other protocols beyond SFTP.
If you're using a Mac, you can also connect to WSO via AFP, allowing you to mount your WSO home folder directly to the Finder. Check out AFP from a Mac (OSX) for more info.