You can use WSUSUtil.exe (found in Program FilesUpdate ServicesTools) to move the downloaded update files (if you are storing them locally) and reconfigure WSUS to use that location for future updates. The procedure is this:
wsusutil.exe movecontent [path to new location] [name of log file]
If you so desire, you can also add the -skipcopy switch to reconfigure WSUS without physically moving the existing files.
To see the full information on the WSUSUtil, visit the TechNet page for it here.