We need a bit more information. Exactly how are you turning the 2D objects into 3D objects?
You can have numerous objects in a single 3D scene and move them independently. They can share textures or have individual textures.
You can make each layer into 3D individually then use Merge to bring them into one scene.
In addition, if they are simply extrusions from paths or shapes you have drawn, then having them on one 3D layer is no barrier to keeping the shapes editable. You can click on the object in the 3D panel then go to the properties panel and click the Edit Source button to open a psb document with the original path which you can edit.
As an alternative you can render each 2D layer separately - but there will of course be no interaction between them so, for example, a glow from one object will not light another.
Thank you so much! You have been very helpful