I’m guessing you’ll need to do a multi-pass render so that you’ll get an alpha-channel pass of the C4D objects, then you bring that into AE to composite it so that it looks like the AE shape layer is sitting between the C4D objects.
Do a quick good of multi-pass render and alpha channel if you don’t know what I’m talking about. I think GreyScaleGorilla has some tutorials on this subject too (but I could be wrong).