My cat introduction story:
When my husband and I met, he had two cats: Flounder, the most good-natured cat in the history of cats, and Gizmo, a captured feral cat who was terribly skittish around humans but a cat-social *dynamo* (we guessed he'd fathered about half the neighborhood strays before DH trapped him). Gizmo and Flounder were BFFs.
I had one: Lola. Lola is my heart, but she was...a problem. She is a fantastic one-person cat, in that she loved me more than anyone in the history of ever has loved anything. No lie--our eyes met at the shelter, background music swelled, and that was it. She hated DH at first, because he took me away from her. Eventually, she learned to tolerate him (and, still, he's literally the only other person she tolerates; if anyone else touches her, they get bitten), but we were worried about introducing her to the boys when we moved in together. Competition.
Lola moved in first; she had about a week in our place before we brought the boys over. We did the separation thing for awhile. Then, one afternoon, Lola was napping on a windowsill. Everything seemed super mellow, so we decided to let the boys out. Gizmo was smart and stayed hidden under a chair. Flounder, however, wanted to play, and there was a new cat to play with. He walked up to Sleeping Lola and swatted her tail. Shockingly, that didn't go well. Basically, Lola turned into the Tasmanian Devil: a quickly moving tornado of anger. She was literally running full-speed into walls, making demon noises, she was so pissed off.
They had a few more encounters that ended with Tasmanian Devil fights (one of which involved DH getting a terrible scratch that needed stitches), and we realized they needed to be permanently separated. The apartment was nicely divided with a french door diving the bedrooms from the living space, so we switched them every day. When Lola slept with us, the boys got the downstairs, and vice versa. They'd scream at each other through the french doors, but it worked pretty well.
A few years later, we moved to a place where it was much more difficult to separate them, so we decided to integrate the cats. We put up the feliway infusers, and we leashed Lola to "re-introduce" her to the boys. Guess what--she didn't care. Flounder walked up to her, and she turned away. Gizmo lay down next to her, and she cuddled up next to him. Apparently, they'd made peace with each other without ever being in contact over the previous three years.
At this point, ten years later, the cats are all old and cranky and sleep all day. Not, like, together, huddled up in a ball, but they've found a nice balance. At night, Lola sleeps in between us; Gizmo sleeps next to my head, and Flounder covers one of us like a blanket. Yes, they occasionally swipe and hiss at one another, but it's never really aggressive. We never thought they would even tolerate being in the same room together, but now, they don't just tolerate each other, but seem to like each other.
tl;dr: It can totally work itself out, with time.