I understand what you're saying but I don't think it's possible. Since the annotations are in a separate file, there is no way to automatically merge them.
The only way I can think of would require you to carefully sew the two pieces together which might drive you crazy. You would have to rebuild you pdf by taking the original, reprinting it to pdf in pieces:
original pdf page
annotated note page
original pdf page
original pdf page
original pdf page
annotated note page
and so on, and so on, and so on
If it's a pdf with few annotations, it might not be so bad but if you have a lot... crazy time!
There are those (like HarryT), who could probably instruct you on how to build a book with your annotations as footnotes. A book would be easier to adapt and update than a pdf (I think).