There is no proscriptive way to how and where one might use the links. But…
Create 2 libraries, Annotated and Originals
In the Annotated library add a column called
original/Original Book.
In the Original library add a column called
annotated/Annotated Book.
Add a book to Originals and copy its
show Book link to clipboard
Copy the book to the Annotated library
Go to Annotated library and put the link in the Original Column
Now you might want to copy the link to the Annotated PDF, flick back to the Original by clicking the Original link in Book details and put the PDF link into that into its Annotations column
I've requested your PM be enabled so I can send you a PM with a link to the two libraries
BR