Just a quick question.. Do you HAVE to remove or move the default kube-scheduler.yaml from the folder? Can't I just make a new yaml(with the custom scheduler) and run that in the pod?
Kubernetes isn't file-based. It doesn't care about the file location. You use the files only to apply the configuration onto the cluster via a kubectl / kubeadm or similar CLI tools or their libraries. The yaml is only the content you manually put into it.
You need to know/decide what your folder structure and the execution/configuration flow is.
Also, you can simply have a temporary fule, the naming doesn't matter as well and it's alright to replace the content of a yaml file. Preferably though, try to have some kind of history record such as manual note, comment or a source control such as git in place, so you know what and why was changed.
So yes, you can change the scheduler yaml or you can create a new file and reorganize it however you like but you will need to adjust your flow to that - change paths, etc.