In the rifle case with the rifle. I don't separate ammo from firearm unless required (overseas travel). Having the ammo without the rifle is just maddening and does you zero good. Having the rifle with no ammo is usually a repairable situation, but not always. If the ammo is with the rifle, then you are good.
I'd rather it all doesn't arrive, or I'm good to go.
Tape your ammo boxes shut with painters tape. They come open sometimes and then you won't see that ammo or the luggage it was packed in.
Jeremy