[Edit]First- Apologies. I wrote this after hours of fighting with Remix. It was written in an angry mindset, was stupidly worded, and really aggressive. The creator did not deserve this at all. [/Edit]

I am having huge issues with layer sprites in Remix. The fact you cant unclip layers either makes this even worse. Does anyone have any tips? I usually work with PNGTuber+, which I am finding WAY easier to use when it comes to layering. Why is the bottom most layer the one on top? Trying to make joints with this program is extremely confusing. In PNGtuber+ I would Link the Hand to the Lower arm, and Link the Lower arm to the upper arm, then link the upper arm to the torso. In Remix it is reversed?And If I want multiple things linked to the torso, it has to be the bottom of everything????

I have the Z set up, but with linking layers the sprites will ignore this number which is annoying as all hell. If I accidentally link something, I cant break it. I tried importing my PNGTuber+ to try to make organizing easier, but this issue still persists, and is even worse :(

The layering system works exactly like in PNGTuber+ and Live2D, more towards the Live2D implementation since it is more accurate to what is actually happening in your model. Keep in mind this is NOT a Drawing Software.
You can unclip by dragging the layer on on another or on the "Model" on the top most part of the layers tree, BUT this was something not everyone caught on easily and a new more obvious unclip button is coming the next update. I have zero clue what you mean in the Z-index part. If all Z-orders are on zero, the order will react by the child's order in the tree, modifying the Z-order in the properties is a modifier, it will ignore the actual position of the child on the layers tree. Please, despite this software being originally a PNGTuber+ fork. A lot has changed along the way and I rather you treat it as its own thing. Not for me, but for your sake. The only things this software still share with PNGTuber+ at this point are the x-y freq and amp. Everything else was changed completely.

I am really sorry you are having issues with the software. One of the reasons why the next update (Aka V1.4 at the time of writing this) is taking so long isn't because of life reasons only, but because I want to try improving it as much as I could. However, you should still understand that something like the layers tree ordering (being bottom to top) wasn't a mistake nor badly implemented. This is what software like this, Live2D, game engines, etc.. use as standard

Otherwise, yes. The software does have its issues and I am still really embarrassed that I even released V1.3.5 in this state.

So the help you are looking for are :

- Drag the sprite you want to unclip on the top most "Model" tree layers root.

- Z-ordering is a modifier, if you want more "natrual" Z-ordering, don't use it; keep it at 0 and just mess with the layers order in the tree.

Also, side-note, the PNGTuber+ import will get a complete update. Not too sure if I will be able to finish it when V1.4 releases, there is a massive chance it will be disabled there until V1.4.1. Take a little breather and I am here to help at any time. No need to stress much :D

Glad this thread came up in a search.

This response helped me to understand how this style of layering works, as someone who has been using drawing apps, which function solely on the order that layers are displayed on a list (krita, et al). So, thank you for responding to their question, it was a very frustrating problem because it really felt like either I was missing something (which I was) or something was broken. -jj

edit: Wait this was AN HOUR AGO? It was like the fifth result on google. How