To address the issue of overlapping transparent effects in a Three.js environment when using Spine, you might need to adjust the rendering settings or the way you manage transparency and depth in your scene. The problem you're encountering could be related to how Three.js handles transparency and depth sorting, which can be complex when dealing with multiple transparent objects.

One approach to consider is adjusting the SkeletonMesh.zOffset value, as mentioned in the context about attachments disappearing or blinking in Three.js. Increasing the SkeletonMesh.zOffset value can help manage the depth sorting of your Spine animations, potentially resolving issues where transparent areas block other effects. The correct zOffset value depends on your scene's depth and the type of depth buffer you're using.

Another aspect to look into is how you're handling blending modes in your Spine animations. Ensure that your blending modes are set up correctly for the desired visual outcome, especially when dealing with transparency. Incorrect blending modes can lead to unexpected visual results, including issues with transparency and visibility.

Lastly, ensure that your Spine and Three.js versions are compatible and that you're using the latest versions of both, as updates often include fixes and improvements for rendering and performance.

In addition to what Spinebot said, could you describe, possibly with screenshots, what exactly you mean with 2 effects?

If your skeletons has attachments with transparent areas, then you will run into issues with the z-buffer, and as Spinebot said, blending. As soon as transparency is at play, you have to render all attachments of all skeletons back to front so blending works correctly.

This is not something spine-threejs can provide out of the box I'm afraid.