I am a bit confused because I don't have the design in front of me. I suspect that seeing as you can only select "Layers to Preview: Top Layer - Bottom Layer", that you must be using blind vias to connect top and bottom to your power planes. I would guess that you don't have these vias set up correctly. Once they are setup up correctly you should be able to select them in "Layers to Preview:". If the pcb manufacturer really wants to know which pads are vias and which are just thru holes then make all the vias the same size and don't make any other thru holes that size. Hope this helps.