Marty, I have no experience with PE Zimmerit, but the problems you are mentionning are the main reason why I stick to either engraving directly into the plastic (smaller scales) or Milliput... I'm not certain the PE brings that much more 'realism' that 'traditional' methods and after all, you'll still need putty in some areas and at the joints between the various PE plates...
As for drilling holes, that's what I would just do, drill them with a mini-drill.