Combine pdf + html files

Hello
I am familiar with how to combine several pdfs into one pdf, and I love the Bookmarks as a built-in navigation panel for my project.
Now I'm trying to integrate the next step. 
My goal is a cd with 3 items in the navigation panel: 
book 1 (from a pdf)
book 2 (from a pdf)
Genealogy
I have a folder with a bunch of HTML files, and sub-folders with other HTML files (they were all nicely generated by the genealogy software I use).  I know that the primary file that runs the series of HTML files is called index.html
I can easily combine the 2 pdf files, and the index.html into 1 master pdf.  But that seems inadequate; the other html files are not in the combined pdf, and the links from index.html to the other files die.
Should I be using Portfolio?

Thank you for your feedback, but I think I need to clarify, and update.
For the moment, I am not trying to create a site.
I am trying to put PDF files and a tree of HTML files/folders, all onto one CD
With a menu to navigate.
I have solved this by doing the following:
- on my desktop, I have a folder (eg, TEMP) which contains the pdf files, and the lead HTML file (INDEX.HTML) as well as its subordinates
- within that folder, I made a pdf that combined the multiple pdf files, and saved it (let's say I called it Menu.pdf)
- I opened the Menu.pdf file, and, in the BOOKMARK panel, I added a bookmark, whose action is to open the INDEX.HMTL file
- I burned the TEMP folder to a CD
The end result when I load the CD is that 2 items show up in Finder:
- Menu.pdf
- folder with my html hierarchy
When the user opens the Menu.pdf file, they Bookmark Navigation Panel gives them options like:
- History (which opens the Family History.pdf)
- Recipes (which opens the Family Recipes.pdf
- Genealogy (which opens the INDEX.HTML file within the folder, and the all the subordinates are linked properly)
Granted, I may not be explaining it with every nuance.....  and it took me 5 CDs to get it the way I wanted it.  But now it is exactly what I wanted, so that 's good!

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