So,
I'm using the house for anvil that I guess never got used. AnvilLCHouse03. In any case the 2 floors of the interior don't line up and I really don't want to make a separate cell for each of them because I don't want the loading screen when traveling to another room in the same house.

So I just kept them separate and put a door that teleports the user to the other door in the same cell. However When I tell the NPC to travel to the other floor they'll follow the grid path until they get to the door and then they'll just walk back and forth in front of the door. However if I go through the door and use the wait option then the NPC manages to be in that room just fine.

How do I fix the glitch where they just have a brain fart and don't know how to use a door? Or do I really need to put the two area's in separate cells? Or will there even be a load screen from separate cells?

I guess in short.. what's the best way to go about doing this?

You need to use a http://cs.elderscrolls.com/constwiki/index.php/SubSpace.

You can see an example of one in the cell "ChorrolCastleWallTowerNE". It appears as a light blue wireframe box.

Awesome. Thanks for the tip. ^^