Separate containers. I’ve called the NJSP and described the following:

I have a bag that has a center compartment, I place ammo in it. On the sides there are pockets that hold handguns and magazines. I can lock them all. Can I use the single bag?

Yes. Below is the example of what I have and described.

Tactical Gun Range Bag, Deluxe Padded Weather-Resistant Shooting Range Bag for Handguns Pistol with Many Rooms Light-Weight(Black) https://www.amazon.com/dp/B076Q7WTFM/ref=cm_sw_r_cp_api_glt_fabc_CQAWRZRZ2T4MEEBMRJB9