I've set up the mannequin exactly how the forum here, as well as youtube, says to. The only problem is that once in game the mannequin doesn't show up, but the "activate mannequin" pop up does (where the mannequin should be). Any suggestions?

Your mannequin has probably moved when your enter the cell. A mannequin is an actor and when the cell load, it will be placed on the navmesh near the point he is in the editor (if your cell have a navmesh) and then move to his editor place, play his idle pose and freeze (deactivate his IA by script). If he can't reach his position, the game will try to move him again, and again until he reach a position near point (0,0,0) of the cell. If there is no place to put him there, the game will simply forget him (or send him anywhere else in tamriel, I don't know).

If his position in the editor is just under the floor, he can fall in the void, but if the script deactivate his IA before moving him somewhere, he will stays there (in the void). To put your mannequin exactly on the floor, you can select it (and the triger and the marker) press Z and click to raise it above the floor and then press F to put everything on the floor.

To find him, you can use the TCL command in the console and move around your cell (you can pass through wall with this).

If you activate the trigger where the mannequin should be (place something or not) then exit the inventory, the mannequin can be replaced where it should be. But if the cell navmesh avoid the travel of actors to reach a place near his editor position, the IA will be unable to replace it there. Your mannequin could placed near point (0,0,0) of your cell. You should correct the navmesh and test it with playermannequin to verify this. If there is some navmesh outside your wall, the game can put any actor there, and they can't reach their position after that. And you can't see it.

Another useful console command is TWF to toggle wireframe. With this, you can see everything easily.