Omega-3 Improves Your Pet Health

i adopted a retired breeding female cat 3 months ago. she is EXTREMELY difficult..food,litter,being touched, about everything and anything. I tolerate her behavior becuase I love her. She hates my boyfriend who lives with me. She still runs away everytime he gets up or tries to walk near by. She only lets me pet her only certain time of the day. She will not sit on my lap but will always be near me.
Due to her anti-social behavior, I got a male kitten thinking she would prefer a company of a same kind rather than humans and boy was i wrong! Ok, so she hisses and hits back but problem is now she pees outside of the box in 2 seperate spots. She does not have any health problem. i clean her box like a nut every day. Her litters did not change. Now she doesn’t even let me pet her nor brush her. She may let me for 5 seconds and then gets all irritated and runs away or paws me.
New kitten boy is doing great. Nothing fazes him and i know he can handle it. As for me, i can not. My darling female cat is exhausting me. if i leave her alone to let her have lone time, she gets upset. She sits and looks at me with a combination of a frown/sad face. If i approach her to pet her, give her snacks or brush her, she gets irritated. Last night, she cried for 2 hours straight. I got up to comfort her but she runs away.
i am sure things will eventually improve between their relationship but i really don;t think my relationship will change. Ever since she came into our household, we bonded but it is just spirialing downwards from here.
Any suggestions on what to do?
(additional info)
Female cat is 5 years old. She got neutered 4 to 5 months ago.
i live in a small open space apartment. i do not have another room to seperate the 2. I initially did for first 3 days by locking up the kitten in the bathroom but i don;t do that anymore. it is not fair to my boy kitten.
again, i am more worried about my relationship with her and i. Those two cats will eventually somehow co-exist. i just need to know how i can handle this monster for now. i try to spend lots of time with her but she won;t have it. when i do entice her with a cat dancer and play for a little bit, she seems to be happy for few seconds and then frowns (of couse when kitten appears to play with her)
What do i do?