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Whenever I try to use items with other types of items, the layering of the items screws up. For example, I have a bridge. First, I put the Twisted Tree (the brown vine thingy) and then put logs on top of it. It looks fine in the LD, but then, in the level, NOPE, the logs go behind the tree. I don't know what's happening, but if anyone has a solution please post it here.

Oh, it might be worth to mention that the layering glitch happens to some of the logs, which puzzles me even further.

Some items like the Twisted Tree automatically override the overlapping of other items.

So basically a Twisted Tree will always appear in front of anything else you place over it.

Layering issues are a very well-known, old, and irritating bug that pretty much everyone already knows about. There aren't many ways to fix layering issues, but things that are known to help include:
*Placing items in the order you want them from back to front
*NEVER using the item eraser tool, instead moving items to unreachable places or removing them in the code
*If all else fails, moving items around in the code sometimes works, but also can make things worse.

Why never use the eraser tool? Does it screw up other items?

Also I would believe that twisted tree overrides every other item, if not for the thing I've attached. The green square shows that the log is in front of the tree (and how it should be), so the tree cannot override everything.

Yep, the item eraser screws up item layering for some reason.

I'm probably gonna find myself wrong, but it is starting to seem like the reason the Eraser Tool does this is because the order of the items in the code is undetermined, until the code is copy/pasted. Removing an item in-game may be "confusing" the game, but if you remove it by editing the code, the game is already recognizing the order things should be in. However, since there isn't a set layering order, unlike Last Legacy, the game assumes what should be over what, and everything may be overriding each other in patterns that cannot be tracked, since we cannot see where the areas of layering are actually taking place.

From experience, this is how it seems to me. But, I'm probably going to be disproved.