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Multi-Cat House: Litter box and Behavior Problem?

Question by Josh: Multi-Cat House: Litter box and Behavior Problem?
Background: all cats fixed - my two males and her female
Chuii - My first cat, 2.5 years old, muscular, graceful, intelligent and gentle black male. I think he is dominant because he seems to win the play battles, but he covers his poop.
Halsey - My second cat, 2.25 years old, chubby, clumsy, and huge pawed orange lover boy. He spent the first 6 mos of life in the humane society kennel, so lacks agility and he is kinda slow-witted. He alway loses feeding rights to chuii, and seems to lose the play battles. But doesnt always cover his poop.
* when I introduced them, chuii hissed and cornered him for 5 days, then I came home one day and they were all cuddled up and best buds ever since, that was almost 2 years ago and they have been well balanced ever since. I believe Chuii is dominant.
Now my girlfriend moves in with her cat one month ago...
Ontario - her cat, 4.5 years old black female, small, thin and crazy. Has not allowed anyone to rub her belly since she was fixed. Bi-polar - will be purring and affectionate one minute and ears back attacking an arm or a leg the next, kinda vindictive of perceived injustice, has been left completely alone often and for 3-4 days each week.
(we are both in the airline industry and are gone for 3-4 days a week, It was my hope that Ontario would be glad to have two brothers to play with while we were gone.)

When she moved in we kept her in our bedroom, door closed with food, water, and litter for one week to get comfortable. We then left the door open to let them get to know each other for another week. I then took away her personal food and water and moved the the extra litter box to a hall closet as they had become community property anyway; and we do not want them in our bedroom.
We let them work it out on there own for the first couple of weeks by not trying to interfere too much and I figured that they would establish a pecking order and soon begin to calm down.
Since then she has sorta claimed the bedroom as her domain. She hisses and growls almost anytime she sees the boys. Chuii never approaches her and just sits and stares, but Halsey, goes right up to her and agitates her until she is cornered and swinging. She has made under the bed her spot, and halsey would follow her under and get into close quarters combat. So we blocked off under the bed and reduced the locations for close combat throughout the house. Amazingly, when Halsey attacks her, Chuii attacks Halsey and then sometimes her too. Chuii usually just commands the high ground, but will often leave the bed if she comes up. Ontario usually sleeps on my chest and the boys at my feet at night.
When she growls and hisses at Chuii, he will just sit there and stare and eventually lie down and sleep. When it is Halsey though... he used to go right up to her and meow forlornly, then he began to take slow swipes at her, now he just usually runs away and stares.
SInce we moved the litter, food, and water: we have to take her out to it and we dont know if she is leaving the bedroom when we are gone on a trip. The real problem happens over the litter box, even when the litter box was in our bedroom, Halsey would run up and start swinging at her when she used it. It only got worse when we moved the litter box outside of the bedroom. We put the boys swing doored box in the living room, and her open doored box in a hall closet, it was opposite at first but I thought the extra privacy would help her, maybe it scares her to be trapped, but we do not live in a large apartment and two litter boxes for three cats seems to be enough plus we do not want a litter box in the bedroom.
When we put her out in the living room she stays firmly in the corner or under the couch for hours then makes a mad dash for the bedroom, and of course Chuii chases her but will stop when she is cornered and hissing. She keeps finding a way under the bed no matter how much stuff we block it with and will stay there for a very long time.
We have tried giving equal attention to them with petting, talking, feeding treats and playing with toys while they are all in the same room. She will not play with toys with them around and she will not move forward an inch to get a treat when they are near. She will go to attack us when we touch her rear, while they are nearby too. Now, I have been calm and assertive throughout this charade and I started to scruff her and use my fingers to "bite" (gently of course) her neck when she act aggressive, but that does not seem to work either. We have been equally affectionate to all of them.
Now, the real problem for us is the litter box. My girlfriend caught Ontario about to use a house plant as a litter box, so she put her in the closet litter box and shut the door. We then wrapped each potted plant with plastic bags, because Ontario hates the sound of plastic. That was 4 days ago. We returned home from our trip Sunday night and Ontario came out from under the bed early monda
We reblocked the under bed from her entry and encouraged her to eat, drink and potty, but we do not believe that she pottied. Last night, monday night, Ontario ran under our covers at 3 am, which she has always done on occasion but this time she PEE'D! Luckily the pillow topper protected the mattress, so we can wash that. I put her in the hall closet litter box and shut the door till this morning.
When I woke up, I opened the door and when she came out of her own accord, I scruffed her and put her nose to nose with both my cats, but both of them just sniffed her face and walked away. I would then carry her back over and put her belly up to them, they would leave. If I let go of her she will hiss again or lie curled up in a ball with her tail between her legs. so this is not working either.The little pain is back under the bed again.
I do not know how to make her feel relaxed around the boys, because other than a few spats with Halsey they mostly try to avoid getting close. But they
But they can stare a long streak.
ANY insight that you can provide into acheiving a balance multi-cat house under these conditions would be cherished. Seperation is not an option, because we are both attached to our felines. Additionally, when she moved in we switched from her normal litter to mine. If you tell me to switch back, I will. If you tell me to put her litter box back in the bedroom I will, but not permanently, so please let us know how to tell when the time is right. Thanks for your patience and attention!
Thank you for all the great suggestions. We will start over from the beginning and keep them seperate when we are not home. The litter box is back in the bedroom bathroom, its the only bedroom in our house and where we spend most of our time, so we did not want the litter tracks all over and the litter box in the way anymore, but we will do the change... We always have showed her a great deal of attention, but it doesnt stop her from ignoring us to be mad at them. We also have not purposefully set about to "abuse" her in our "house of horrors". We are both animal lovers and have spoiled her silly. We tried to avoid showing her the favoritism of "living as sole proprietor" of our living space as that is unfair to the boys and they have a right to sleep with us on the bed too. Also, we will try the towel thing too, it sounds like a great idea. It was my hope, before the pee incident, that they could work this out on their own, but will be patient and give it more time. thanks!

Best answer:

Answer by Greeneyed
your leaving them alone for too long of a time, you need a cat sitter
and another litter box(maybe in the bathroom??)

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