EDIT: Here's the answer from guide
"apps dataset that has a dataset under it for each application's configuration files owned by the user that it will run as. "
Ok, well I interpret that to mean the apps dataset is completely separate from the dataset that contains the files for the jail. If they meant jail I think they would have called it a jail dataset, not an apps dataset.
So I have something like this
DATASETS
|
|_ /mnt/tank/video
|
|_ /mnt/tank/apps
| |
| |_ /mnt/tank/apps/nzbget # Mounted to jail and holds the config files for nzbget
|
|_ /mnt/tank/jails
| |
| |_ /mnt/tank/jails/nzbget # Actual jail, this dataset is created automatically by FreeNAS when a new jail is created. Inside the jail there is a folder /config which is created by mounting the /mnt/tank/apps/nzbget dataset. This /config folder holds the apps config files and is linked back to its original location.
If someone who knows could say if this is right or wrong that would be great. Thanks!