Still having trouble introducing two cats

My fiancee and I have two cats: Ellie (a year old, we've had her for about 4 months now), and Theo (almost 2 years old, we got him about 2 months ago). We royally messed up introducing them when we first brought Theo home. Now I'm starting to be afraid that they'll never get along. 

It has come to the point that we have separated them, just in an effort to keep them from fighting and make things easier for everyone. Ellie now has the basement to herself, and Theo has the upstairs to himself. They each have separate food bowls, litter boxes, etc. They rarely see each other now but sometimes they accidentally come in contact (mostly through Theo sneaking downstairs) and when they do it's all growling, hissing and fighting.

Although Theo is the newer cat, he's much more outgoing and seems to be trying to be the dominant cat in the house. He knows he can get Ellie worked up and when they have come in contact, he sits there and stares at her or approaches quickly as if he's going to attack her. Ellie instantly gets mad when she sees any glimpse of him and starts growling and hissing - but it's more like she's scared rather than she's going to attack him. Anytime they do fight, it's usually because she feels scared and cornered by him when he approaches her. 

I have never seen them have any kind of remotely civil interaction. It's always Theo being in Ellie's face and she gets upset about it. So the question is.... how can I re-integrate them in each other's lives so they get along? How do I get Theo to stop being constantly in her face? Ellie is actually currently out of the house being spayed (will be back late tomorrow) and Theo has been neutered right before he came to us. I'm thinking her return from the vet can be a point of reintroduction somehow, and trying to do it right. I don't like that Ellie is downstairs all the time hiding in fear, but Theo strongly resists being trapped anywhere so it is better for him to be upstairs if they have to be separate. 

Any advice on how to reintroduce and hopefully get them to at least get along?

Keep them separate for now. Do you swap their area's so that Ellie gets time upstairs and Theo gets time downstairs? This will allow them to explore each others territory and scents without actually meeting face to face. Take their bedding leave it in each others area's of the house for the same reason.

Have you tried running feliway at all? Or a sentry collar each while you do this?

When you feed them feed them on each side of a closed door so they can smell each other. If you have to start with the bowls a metre or two away from the door that's okay, just inch them closer and closer until they're happy to eat on each side of the door. Then crack it open with a wedge so they can see each other and maybe even touch paws but not actually get at each other and they still have their safe place.

Continue to swap their area's daily the whole time.

After they're okay with the door cracked open with the wedge they can maybe try supervised time together (either free roaming or you can do it with one in a carrier).

Bear in mind this can take days, weeks or months and they may never be good friends. My 2 aren't. They tolerate each other but we do have occasional fights and days where I have to keep them in separate rooms on and off all day.

Four months is not long at all in a cats world, it does sound like Ellie needs a 'safe' zone to retreat to when Theo gets into her face. High up and difficult for Theo to attack from any side but one. My Chrissy had a bed on top of the fridge for a year. Sternly say "NO" to Theo when you see him stalking her,  and put him in his separate area if he persists. All the advise above is excellent, it will reintroduce them and hopefully let everyone get to know each other.

It may get better now that Ellie is spayed, she won't smell 'available' to him anymore and may seem less interesting. Even though he is neutered, it was only a few months ago and the hormones take a long time to leave, several weeks to months.

Theo is more outgoing and wants to play, he is still fairly young and hasn't settled down yet. Believe it or not, her hissing and growling at him is perfectly normal, even swipes with a paw. Females are often little divas and want little to do with other cats in the house. She needs a lot of rest and little movement after her spay, so now would be a good time to take the steps mentioned above.

Theo needs to be diverted from her, he needs a toy thrown, or a wand brought out when he starts his staring. If he persists, then a 5 minute time out. Ellie will learn to stand her ground, and once she doesn't run, it won't seem like such fun for Theo, she can't feel like she is cornered. Once my Chrissy finally stood her ground and swiped at the boys, they stopped annoying her. That took at least 6 months.  Growling, hissing, and an occasional tussle are all normal, but if bites or blood is drawn from scratches, that is too much aggression and has to be stopped.  Time is your friend, there WILL be a time they will get along, maybe not as playmates or sleeping together, but peacefully and as family. All the luck!

Thank you both for your help! Your suggestions are great, but Ellie is very scared and nervous and gets super angry when there is even the chance of her getting near Theo. If we try to carry her up the stairs, for example, she freaks out to the point of biting, clawing, trying frantically to get out of our arms, and making loud yowling noises. If we do manage to get her upstairs, she'll go in a corner and hiss and growl even if she can't see Theo (such as when we lock him in another room to try to make her calm down). If we even come near her when she's like that, she'll try to attack us as well. She is a very temperamental cat when she is made to do things she doesn't want to -- another example is that every time she goes to the vet, she attacks the vet and won't stop trying to escape the whole time she's there. I like the ideas, but I'm just not sure how to get her to do some of the things necessary without causing her to freak out even more.