If I am understanding your correctly, you are saying that after you set up your ProAnimator scene, then come back into the After Effects Comp, part of the scene is missing. If this is correct, then this means you have applied ProAnimator to a Solid Layer that is not Comp Size. ProAnimator should always be applied to a Solid Layer that is Comp Sized. If the Solid Layer is not Comp Size, then you will run into clipping issues where parts of the ProAnimator scene do not show up. To make the Solid Layer Comp Size, simply select the Solid Layer, then go to the Solid Settings window and click the "Make Comp Size" button.
Once you apply ProAnimator to a Solid that is Comp Size, your ProAnimator scene will fit perfectly with the After Effects Comp.