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Here's a few easy steps you should follow to make the switch:
1) Uninstall the SETI@Home Screen Saver version. Keep the WU and the SETI folder.
2) Click HERE and scroll down the page and download i386-winnt-cmdline.exe to your SETI Directory.
3) Start the CLI ("i386-winnt-cmdline.exe").
4) When it prompts for 1 or 2, enter 2.
5) Enter the email address you used with SETI@Home.
6) Now it will start over on the workunit you gave it then continue normal operation.
You can run the CLI with other programs listed in the Programs section. It will not affect your CPU time.