So here is what you need to do starting RIGHT NOW!
First of all, no more covering her cage AT ALL until it's time for her to go to bed. That's it. You just simply CANNOT put that cover back on her cage during the daytime! Period!
****What you need to do starting right now, TODAY, is to put her on a "Natural-Light Schedule", you can start it right now by taking the cover off of her cage immediately, and making sure that wherever her cage is located allows her to be able to see the natural light-changes with the Sunrise and the Sunset (meaning the light-changes of the Sun are visible in the room she's in, so she will visually know when the Sun is setting in the evening and when the Sun is rising in the morning)...So regardless of what time of the year it is, she needs to be able to see the natural-light changes of the Sun in the evening, and right as the Sun completely sets, that's when she must go to bed, so put the cover over her cage ONLY after she sees the Sunset...And then she must have the cover removed from her cage right as the Sun BEGINS TO RISE, so that she is able to see the light changes of the Sun as it comes-up in the morning. And then you just have to keep the cover off of her cage ALL DAY LONG, EVERY DAY! And again, it doesn't go back on her cage until right when the Sun sets, and it must come off right as the Sun starts to rise.
This is called a "Natural Light Schedule",and it mimics exactly when birds/parrots naturally wake-up in the morning, with the Sunrise, and when they go to sleep in the evening, with the Sunset. That's why you start hearing the birds outside chirping/talking/singing so early in the morning every day, right when the Sun starts to come-up, and also why you stop seeing or hearing birds after the Sun has set (except for nocturnal birds like Owls). This not only puts them on a completely natural waking-and-rising cycle with the Sun, which keeps their sex-hormones at-bay, but it also ensures that they get at least 10-12 hours of sleep every single night, which also keeps their sex-hormones at-bay.
And obviously you cannot EVER cover her cage up during the daytime when she's supposed to be awake, because what happens is exactly what has happened with your bird, their sex-hormones are triggered and released, and if you continually put her on a waking-and-rising schedule that is THE COMPLETE OPPOSITE of what their natural daily cycle should be, it puts them into a constant state of Breeding-Season...It also totally confuses and messes-up their Circadian-Rhythms, and pretty much every other natural process that is supposed to be going on inside of their body and their brain.
****Also, keeping a bird covered like you have pretty much 24-hours a day for months and months has for sure caused her a Vitamin D Deficiency, among other Nutritional-Deficiencies and physical health problems, because you've basically deprived her of any natural sunlight at all for an extended period of time...And these physical health issues and nutritional deficiencies and the syndromes/side-effects that they cause has no-doubt also added to her aggressive and strange behaviors.
Something that you need to know and always keep in-mind for not only your Amazon but also for your Cockatiel and any other Parrot/Bird you might add to your family in the future, is that they are not at all similar to keeping any other type of pet, not in any way! All Parrots have the intelligence-level of a 2-3 year-old Human Child. They use logic and reasoning skills, and they have better long-term and short-term memories than we do! And this includes your Cockatiel and all other species of Parrots, from the Parrotlet and the Budgie all the way up to the Macaw and the Cockatoos. So this makes them extremely sensitive to ANY KIND OF CHANGES in their environment (your home), and also within their Flocks (them, you, and anyone else who lives in your home is their Flock). They are natural Flock-Animals, and so their Flockmates are extremely important to them, and as such, ANY CHANGES TO THEIR ENVIRONMENT OR THEIR FLOCK are going to cause them to feel stress, anxiety, and will cause them to act-out and display changes in their behaviors and their personalities UNTIL THEY HAVE TIME TO SETTLE-IN TO THE NEW ENVIRONMENT AND GET USED TO THE CHANGES, BUT THESE CHANGES IN THEIR BEHAVIOR, THEIR PERSONALITIES, ETC. ARE ALL TEMPORARY AND WILL RESOLVE THEMSELVES! So when you brought home the Cockatiel, this certainly would have caused her some stress, anxiety, and since every bird is an individual, just like people, they may show this stress and anxiety and displeasure with the changes in any number of ways. So yes, she probably did originally start screaming a lot and acting-out due to the new Cockatiel in her home/Flock, but this would have gradually gotten better over-time as she adjusted to the change, just like we as people need time to adjust to changes. With Parrots it's all about giving them enough time to work through things and get used to changes.
And from now on, if there are any large changes to your home, to the people in the home, to the pets in the home (whether they are birds or other animals that come into your home), or changes to anything else that effect her OR THE COCKATIEL AS WELL, you need to approach each time this happens as a different issue, and then try to figure out what you can do to make things better for them regarding that particular change. That's when you come here and ask questions about how to stop your bird from constantly screaming like she has been since you brought home a new bird, or whatever the problem is.
I understand that you figured out that covering her cage and keeping it covered all the time it stopped her from screaming, but obviously that wasn't the right thing to do. Sometimes as a parrot owner you have to simply put-up with a screaming bird for a few days or even a few weeks, as once again, they are not dogs or cats or any other type of pet due to their intelligence levels (only pet Primates like Monkeys and Lemurs are as intelligent as Parrots are), and Parrots just simply do not respond to any type of punishment/Negative-Reinforcement, this only makes their behavior and attitude worse and worse and makes them more and more aggressive. Instead of punishment/Negative-Reinforcement when your birds do something wrong or display a behavior you don't want them to, you need to TOTALLY IGNORE the bad behavior they are displaying and pay absolutely no attention at all to them every single time they display the bad or unwanted behavior until they stop doing it....And that could take a few minutes of ignoring them completely and pretending like they don't exist, a few hours, a few days, a week, etc. It's very much a "Battle of Wills", and it comes down to will she stop screaming first, or will you stop ignoring the screaming first and start paying attention to her first. And once you win the battle, the behavior generally changes very quickly because the thing they hate more than anything is being totally ignored by their person and having their person act like they don't even exist.
And then in order to get them to replace the bad or unwanted behavior with the behavior you want them to display, you need to Positively-Reinforce the bird displaying those good/wanted behaviors by giving them a "Training-Treat" every single time they display them (a "Training-Treat" is whatever treat is your bird's absolute favorite treat, and it's very important that they NEVER, EVER get that very special, favorite treat at any time other than when they are being rewarded for displaying a wanted/good behavior...It should be something that they not only love more than anything else, but something small that they can eat quickly and that you can always keep in your pocket whenever you're at home with the bird)...
***The reason that your bird stopped screaming when you covered her cage up is because it instantly created a small, dark place and triggered the release of sex-hormones. And while it did stop her from screaming, not only was it a completely horrible thing to start doing due to the risk to her health and it putting her right into Breeding-Season and kept her there the longer you did it, but SHE ACTUALLY TRAINED YOU!!! She learned right away that if she started to scream it would cause you to cover her cage up.
I know you didn't realize what you were doing/causing to happen, nor were you aware of the risk to her health and well-being...But now you know, and you need to immediately take the cover off of her cage and keep it off. And you need to remember that it is probably going to take at least a good couple of weeks to knock her out of Breeding-Season, stop the aggression, and stop the screaming (or whatever else is going to happen once you keep her uncovered. So you and the others in your home are just going to have to put up with any screaming, and make sure that you and everyone else knows that as long as she is screaming you all need to TOTALLY IGNORE HER, DO NOT TALK TO HER, DO NOT MAKE EYE CONTACT WITH HER, DO NOT GET FRUSTRATED AND START YELLING AT HER, AND MOST OF ALL DO NOT PUT THE COVER BACK OVER HER CAGE! And if she does start continually screaming and you are totally ignoring her, and then she suddenly stops screaming for at least a minute or two, THEN you need to go right to her cage and verbally praise her and give her a Training-Treat. And continue to do this every day, all the time, and gradually the sex-hormones will leave her body and things will go back to normal.