Does anyone have any advice for us?  

Bless you for answering this! Thank you! Our cats do have separate litter boxes. I found this necessary when the fighting began. As Clarissa stays under the bed all day while Cougar (also female) is upstairs, they still have the same food dish, because Clarissa comes out to eat and use the litter box after I put Cougar downstairs to sleep. Cougar is basically our daytime cat and Clarissa is our nighttime cat. Poor thing!
I've taken some advice from Cesar Milan, the Dog Whisperer, and use my fingers as "teeth" to let Cougar know I'm head of the pack. I don't hurt her, I just let her know that I'm the boss. She has become submissive to me, yet she still attacks Clarissa. I've heard of the water bottle technique but have yet to give it a try.
The other problem is, though, that even when I put Cougar downstairs, Clarissa is very hesitant to come out and is nervous for the first half hour of coming out from under the bed. Even if I get control of Cougar, Clarissa has really become a "fraidy cat." I feel so bad for her!
Thank you for your response!!

I wish there were more that I could suggest and if I do come across something, I'll send you a message through mylot. I have heard of the dog whisperer and like his training methods; it is such a great idea that you are trying to establish 'rank' in the house by baring your teeth to Cougar. I will have to remember that. I know this is not fun for you or Clarissa so I hope my suggestions are of some help. Take care and have a great weekend!