Generally, in my experience, modifying the backing storage for a nextcloud instance is more of a PITA than its worth. I would just mount the webDAV in your file manager. This way the nextcloud db stays in sync with the backing storage.
If you are going to be making direct modifications to the backing storage, check this form post on modifying the nextcloud config to have it look for changes on the filesystem.
As for the permission side of things, run ls -lh in the folder that you want to make changes and see what the user:group is for ownership of the existing files and make sure your new files match. Chmod and chown will be your friends here and chmod has a --reference option that let's you mirror permissions from an existing file, a real time saver.