In a plotscript, how does it know which NPC 2 to use, if there's a new list of NPCs for every map?

The plotscript will run commands that affect maps (tiles, NPCs, etc) on the current map. So, if you had a script like this:

script, foo script,begin
 walk npc(2,left,3) # NPC #2 moves 2 tiles to the left
end

And you ran it on the map "Barville", then the second NPC on Barville will move two spaces to the left. If, at some point, the current map becomes "Another place", then running the script will move the second NPC on Another place.