I found a temporary fix for anyone interested.
1. Configure Deluge so that is exactly as you want it.
2. (Make sure you have the CA Backup / Restore Appdata plugin installed) Backup your docker data | MAKE SURE TO LEAVE DELUGE ON | (either backup all the dockers or just deluge).
3. Navigate to your backup, unzip the backup, copy the entire deluge docker backup folder.
4. In UnRaid, stop the deluge container, remove the container (make sure your have 'also remove the image' is checked)
5. Navigate to your Docker data/share (make sure deluge is shut down and removed). Delete the entire deluge docker folder. Paste in the deluge docker folder you copied from step 3.
6. In UnRaid, add container, navigate your ('my') containers, select the deluge one, assuming all settings are correct, hit apply.
7. Deluge will probs auto start, and you should be good to go!