So my conure and my baby quaker keep fighting on the top of the quakers cage but they tend to fight less anywhere else. It’s usually the quaker that I think gets territorial of the top of her cage. What can I do to fix this?
It's pretty common for Quakers, or most parrots for that matter, to exhibit territorial mannerisms and honestly there's nothing wrong with those behaviours. Being protective of their territory, resources, and home are survival skills that are present on a genetic level. Instead of aiming to resolve all the resource guarding behaviour I would instead aim to help the conure realize that isn't an okay place to land and help your quaker learn that if they do land there you will help resolve the issue and they don't need to escalate things.
You can place barriers to make the cage not have any direct flight paths which will deter the conure from landing while you work on creating more positive associations with appropriate landing zones. Over time interest in landing on the cage will dissipate as it lacks value and the barriers can be removed as they favour new more enjoyable landing spaces. You can help this along by treating them for landing in appropriate spaces, setting up foraging activities or play sets with toys to encourage fun activities in these other spaces.
From the Quaker's side of things I would have the conure on your hand or in a carrier if they're likely to jump off, and give the quaker a treat as you approach with the conure, immediately leaving afterwards. Each rep you bring the conure a little bit closer provided the Quaker is comfortable with them at that distance. The goal being to have the presence of the conure near the cage being a cue that treats and good experiences are to follow which can help reduce the severity of the aggression and encourage more calm behaviours with the conure near the cage.
Throughout this process if the conure ever does land on the cage I would immediately remove them, give the Quaker a treat for tolerating that situation, and set the conure up with a different activity to do. This way the Quaker learns that you will help and he doesn't need to aggress to have the conure leave his zone and the conure can learn that being on the cage doesn't yield any fun but there's different places that can.