if I have a eps with 2 shapes a yellow star and a red circle behind that, when I import this into AE using the plugin the star and circle are on the same plane thus overlapping. Is there a way to avoid this or fix this?
I'm guessing that you wish to set different extrusion depth to each contour to make them stand out. That would not be possible with BCC 3D Objects at the moment but is easy with Boris Blue (as an AE plugin). If you send me your EPS sample (email@example.com) I'd take a look.