ULTiMATE what an interesting idea. I'm a little confuse about what your asking, but I'll give it a try.
Setting up the comment table with a page id, section id, and position fields (assuming you need to save the position) would provide the information you need to associate the information. It would also provide enough information to sort and filter them if the need arises.
In terms of the layout, if the sections were a page or longer, paginating the sections with a comment at the end would make sense.
If they are shorter, a lot of comment fields would be distracting. In that case, one field at the bottom would be a catch all. A comment icon at the end of each section could expand to a comment field. Comments could be placed in a side panel as notes in the margin.