What is a persistent reference?
I know sometimes things don't work if that box isn't checked... but I don't know why, and I want to make sure I know so I can utilize it to its full potential.
A persistent reference is a reference that needs to be manipulated or accessed somehow when the cell you put it in isn't loaded. For example, if you write any kind of script that refers to it, then it has to be a persistent reference. Say your reference is a wolf. If you just want to place the wolf in a cell and have it be a normal encounter with nothing special, then it doesn't need to be persistent. But, if you only want the wolf to appear if certain conditions are set, like a Go Kill This Wolf Quest that includes a script to enable it, like
MyWolfReference.Enable, then it must be persistent.
... btw you should probably only make it persistent if it needs to be.