Right, it's possible to import images/videos into After Effects and apply them as Layer Maps. The advantages of working with Layer Maps is that not only can you use an image or video file, but you can also use an After Effects Pre-Comp. This allows you to set up dynamic content for your material that you can edit or add effects, and will update the material instantly.
It's also possible to set up 3D Layers in After Effects and when you have the "Use Comp Camera" setting enabled, this will help you integrate your 3D elements from Invigorator/ProAnimator with the 3D layers in After Effects. The disadvantage is that the Zaxwerks 3D Space and the After Effects 3D Space is different. So even though two objects may be in the same position, they will not intersect one another. One layer will simply overlap another, depending on the layer order in After Effects.
If you need your objects to intersect, or to interact with one another, it's probably easiest to work with all the 3D elements within Invigorator/ProAnimator. This way all the objects will be in the same 3D Space and you will not have to worry about having to use masks to pull off a certain effect.