I've been thinking about making Blackreach a war zone between four factions, but I want the NPCs to spawn throughout the trigger boxes. Just like the ones in the vanilla CW story.

Question is though, is that how multiple NOCs spawn is by the use of a trigger box? Because I see those boxes alot in the creation kit. I know I may need to research the CW script and copy/paste then reformat it, but I was wondering if trigger boxes are pretty much the spawn points.

No, not really.

Use XMarkers to spawn people. Or better yet, place them in and enable them when necessary.

And just write the script to respawn another NPC after the other NPC dies? Because that's how CW operates