Advice for file indexing / linking?

Good morning,

I am working on a 260 page document composed of many one page individual protocols. The document needs to be used in two ways:

1. One version must be a fully compiled 260 page .PDF document with embedded links referencing different pages.

2. Another version will be uploaded to a website, and will be parsed by protocol into individual .PDFs for ease of access (and to reduce individual file size).

Because we have several people working on this document, we decided to develop each protocol as a separate .indd file. We are thinking that we will be able to combine all of the files as a book to generate the fully compiled document.

My problem is that I need to come up with a paradigm for linking between these documents that will work for both solutions. I am thinking that linking to relative paths would make the most sense, because then the file structure could be uploaded directly to the website to preserve those links.

1. Does anyone know the correct way to place these URLs to relative paths within InDesign?

2. Does anyone know whether these relative paths will be mapped correctly when the book is assembled from the multiple .indd files?

Thank you for your time and expertise!