Element 3D Layer Issue

You should look into working C4D for this (looking at your screenshot)

E3D, while being quite useful has some limitations 

However, as pointed out by both Mylenium and Rick a proper understanding of the software is needed before you begin your 3D journey.

Begin with a single object in E3D and then look at the position tools or camera tools to move things around or in 3D space

Once that has been done learn to use the group funtions in E3D to create multiple grpup objects on a sibgle solid layer with E3D applied instead of having E3D on multiple soilds.

Best of luck

Mo

Hi. Thank you for the Response, I forgot to mention in the Original post that I've also tried doing it all in a single E3D layer as well but no luck with that as well neither did changing the render settings. 

You need to consider every iteration (layer) of Element 3D as its own closed 3D world.  Elements from one layer do not interact with elements from other layers, except for After Effects cameras and lights.  There are lots of tricks you can employ to get around this, but by far the easist approach is to work entirely within one Element interation on one layer.  

There are 5 independently controllable groups within  the plugin, with virtually unlimited objects within each group.  If 5 groups aren't enough, as in you need to independently animate more than 5 elements, you'll need to use a second Element layer, and then use tricks like split layers, matte layers and the Camera Cutoff function in Element to fake the interaction between objects.

You should be able to achieve your design goals if you spend some time on the Video Copilot site looking at the Element 3D tutorials. You should be able to find what you are looking for there. I would avoid searching YouTube because many of the newer tutorials that show up have been by well-intentioned enthusiasts, and their workflows can be a little odd.

Quite generally simply not how E3D works. You have a wrong understanding here. All elements must be set up within the plug-in anbd on the same layer. At best you can try and work with the unified renderer by enabling it in the advanced render settings, but even that has severe limitations on how it can handle nested comps or items referenced across different layers. It's an inherent issue with how AE works on a general level. I'm afraid you need to come up with a completely different strategy and massively restructure your project or use other plug-ins or a 3D program.

Mylenium