I've set up a Software Update Server and pointed clients at it in the JSS. This seems to work fine on most clients, but on a few it's still going to Apple / App Store for updates.
if I run the command to check where it's pointed:
sudo defaults read /Library/Preferences/com.apple.SoftwareUpdate CatalogURL
I get this response every time:
The domain/default pair of (/Library/Preferences/com.apple.SoftwareUpdate, CatalogURL) does not exist
This is on El Cap and Yosemite clients. Not sure if it's something wrong with that command, I'd expect it to return something?