I've fitted a few sets of speakers in the back of Navaras.
You need to take the factory speaker grille off and make up a MDF spacer the same shape as the grille. Then round over the edges, cut a 6" hole in it and trim it in some grey vinyl. The new speaker will mount through that spacer on the outside of the door card.
I don't think i've explained myself all that well so I'll try to dig up a pic.
EDIT:
I couldn't find a pic of a Navara door, but I did find some of a GQ patrol which is kind of similar.
You'll see the spacer is exposed on the outside of the door, covering the factory grille with the speaker screwed to the spacer. Don't mind the weird shape of the spacer, that's just to cover the old speaker hole.