Layers that were invisible on CSP showing on Live2D?

Hello, so I'm brand new to the program and I have an issue that I have no clue how it happened. So when looking at my model through Clip Studio Paint that I did, even though there are parts that I drew underneath others, they aren't visible.

Example:


But then when I import it into Live2D, they show through the whole model. (I have the mouth parts invisible on Clip Studio Paint but the back of the head as well as some of the other parts are visible but don't show the coloring overlap, but then Live2D shows it all.)

Example:


I'm just not sure if it's due to Live2D being set up differently compared to Clip Studio Paint or maybe I messed up doing the parts, any help would be appreciated.

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