I would expect PAF Companion 5.5 to use Amyuni in Preview and Publish modes on your 64-bit computer. That seems to be the way Pierre has designed it. You should be able to use Adobe Acrobat Pro as your "printer" for printed output.
If it is not working this way, maybe see if you can contact Progeny Software directly.
Your Acrobat Pro should allow you to open the PDF documents created by Amyuni and edit them if you wish.