@Junior The JSON files that Templater generates in that folder can be ignored. They aren’t relevant to what you’re doing. You will want to still remove any that got imported into the Project panel in your AEP file, as those can cause errors.
You can have the project file and the replicated AEP files or videos in separate locations. The two are independent. In addition, you can also have the AME watch folder be in a completely different location from AME’s output folder. AME defaults to sorting the files it is processing into a source and an output folder within the main destination that you are watching, but you can set those to be separated.