For the eyes I think your only chance will be to select by material. It will be the only way you can select the polygons within the skull. You may find that defining your groups in your modeling program or UVMapper ( http://www.uvmapper.com ) to be easier.

For the eye joints you'll need to do some editing of the CR2 file in Wordpad or a propriety editor. I use CR2editor ( http://www.poserstuff.com/programs/Cr2Editor.zip ) Remove the joint lines in the eyes and the ones relating to the eyes in the head. Again see an existing Poser model for an example. If you have loaded in an existing Poser bone set up then this will have all ready been done.