Does anyone have any advice for us?

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What do I have to do to get my cats to stop fighting? I believe it all started when I accidentally ran over Cougar's tail with the computer chair. Clarissa was sitting next to her, and I think Cougar associates the bad experience with Clarissa and that Clarissa caused her pain. Now, I have to put Cougar down in the basement at night so Clarissa can come out from under the bed and do her business. Clarissa won't come out from hiding because Cougar attacks her everytime she sees her. Both cats are spayed. It's been going on for almost a year now, and it's just ridiculous! I watch "The Dog Whisperer" and use some of his techniques on Cougar (HAHAHA!) and she has actually calmed down a bit, but she does still harass Clarissa whenever she sees her. They used to be best pals, now they can't even be in the same room together. Any hints on what I can do?