To quote Evan Nappen: "The exemptions in 2C:39-6g require that your gun be unloaded. The ammunition can be right next to your gun, even in the same box case. But don’t have it loaded in any magazines because if the magazine is loaded, they will claim the gun is loaded."
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.