Do Documents Automatically save in Folders They Are Created In
No, documents do not automatically get saved within the folders they are created in when using a template.
Documents will be created within a Clio folder when they are linked to the Matter within Clio and not necessarily the folder it was created in. When the document is created within the folder of a matter name, it will show up there as it was linked to it.
But if the folder is not created by Clio for a matter (it doesn't have a matter name), then it won't show up within that folder.