Iam not sure whats your folder structure, here is a full example ( for ENCFS) with self describing folder names
├─/home/plex/acd-encrypted acd: fuse.rclone
├─/home/plex/acd-unencrypted encfs fuse.encfs
├─/home/plex/upload-unencrypted encfs fuse.encfs
└─/home/plex/union-acd-upload unionfs-fuse fuse.unionfs-fuse
rclone mount --allow-non-empty --allow-other --checkers 16 --max-read-ahead 14G --acd-templink-threshold 0 acd:/ /home/plex/acd-encrypted &
ENCFS6_CONFIG='/home/plex/.config/encfs/encfs.xml' encfs -o allow_other /home/plex/acd-encrypted/backup /home/plex/acd-unencrypted --extpass="cat /home/plex/.config/encfs/.encfs"
ENCFS6_CONFIG='/home/plex/.config/encfs/encfs.xml' encfs -o allow_other /home/plex/upload-encrypted /home/plex/upload-unencrypted --extpass="cat /home/plex/.config/encfs/.encfs"
unionfs-fuse -o cow /home/plex/upload-unencrypted=RW:/home/plex/acd-unencrypted=RO /home/plex/union-acd-upload/
Rclone move command
/usr/bin/rclone move /home/plex/upload-encrypted/ acd:/backup -c --no-traverse --min-age 20m --transfers 15 --checkers 15 --delete-after --log-file=/var/log/rclone-upload.cron.log
So as you can see all encrypted files are stored on acd in backup folder ( and inside you have subfolders for movies and series )
The Plex Library is set to /home/plex/union-acd-upload/ , the CP / SR destination is also set to /home/plex/union-acd-upload/ ( eg union of acd and upload folder )
The rclone is moving encrypted files directly to acd/backup folder.
All you need to do now is translate to your folder names.
I suggest you switch to crypt as its much much cleaner not to mention better to use since it can take ages if CP and SR are moving files at same time as those need to be encrypted on the fly on disk.
With crypt those files would be moved instantly and crypt would encrypt them on the fly during upload.