Resident Cat Aggressive Towards New Cat?

A few months ago I adopted a one year old female cat. She is a sweetheart, but is very paranoid by nature and prefers that you move slowly. She's taken to me a lot more than my boyfriend, who she doesn't like. She gets upset easily as well.

We rescued a stray cat that wouldn't leave our home. He's a very calm and loving male, about 8 years old. He doesn't seem to care that my other cat exists, though she cares. She will growl at him, hiss, and run away. They haven't fought yet, but she hates him. It's been a month now and things aren't changing no matter what we do. We've read countless numbers of articles online. Right now they are separated, as she was screaming at him last night when they were both under the bed. It sounded so mean and cruel, that I separated them in fear of a fight. He would clobber her with one swipe.

What do I do? I love them both, but I am starting to think that our girl cat just doesn't like other cats. We adopted her from a vet, who said she was separated from her sister. The other cats at the vet were able to roam, but my cat was kept in the break room (not sure why).

When do I draw the line that they aren't a match? How do I help her transition? I've tried everything! She gets so upset over small things. She pees by accident when she's upset or afraid.

What do I do?