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I'm not a noob at pathing, just to make that clear. I know how to do it.
I am making a tunnels map, and the paths are going THROUGH the tunnels, not into them or anything. But inside the map, the AI are always running along the walls. It's extremely annoying, as they hardly ever use the paths. How do I fix this?

Put barriers along the walls.

Okay, I will.
And is it possible to have different layers of pathing, if you know what I mean? My tunnel map is 2 stories, one on top of the other.

Nope, planning and barriers have indefinite height. Unless the two levels of your map are exactly the same in layout, it won't work.

also a word about pathing in general pathing tells AI where to go barriers tells AI where not to go. It's kind of a subtle difference but it makes a big impact. If an AI is attacked it will ignore pathing and try to avoid the attack and counter. If there are no barriers it will go anywhere regardless of where objects are or not. However AI will never disobey barriers. Technically you should be able to make a level with only using barriers and without planning but I've never tried it. Anyways the short answer is put in barriers