If you can access the cargo space from the passenger compartment, you should keep your loaded mags in a separate container from the firearm. Both should be out of reach of the occupants.
Both should not be visible from outside the vehicle. Blankets are your friend.
IF YOU ARE TRAVELING WHOLLY WITHIN NJ:
You can travel with loaded magazines even in the same case as your firearm as long as you are in a vehicle with a trunk and the firearm and ammunition are locked in the trunk.
As long as the loaded magazine is not inserted in the otherwise empty firearm, you are good to go during Intrastate travel within NJ.
For vehicles without trunks, and for Interstate travel, the answer will be different.
Ultra conservative attorneys may tell you differently, but the law is the law.
I am not a lawyer, but I have dated a few Holiday Inn managers.