I have an already running enterprise application which stores a lot of documents inside the documents folders. I wish to disable the iCloud backup of all these documents and
Perhaps the files are changing dynamically because they are being regularly updated from a server or similar? If so, then the answer is to move your file storage from the directory to the directory. These documents will not be backed up. This is of course only suitable if the data can be re-downloaded or recreated in the future, if required.
See this Apple documentation for an overview: https://developer.apple.com/icloud/documentation/data-storage/index.html