Placing a PSD Bitmap or Layered Tiff over a spot colour in illustrator or Indesign

I have a cover designed in Illustrator CS4 that has spot colour as its base, and I have designed a graphic with a transparent background in photoshop. Cause I am working in Adobe Suite I bring the CMYK PSD file into Illustrator CS4 and comes in perfectly. The problem I am having is that when I convert to PDFx-1a via print or save as illustrator PDF, the file comes in with only the spot and white area highlighting where the overprint. Please can someone give some assistance to the best way to approach this issue. It is important that it has a transparent background to go over this Spot background. Also I need for the lovely shadows photoshop produces to be present in the Illustrator document without rendering white in PDF. Thank you.