This works best with a PDF that has a table of contents.
- Open the PDF in iBooks.
- Navigate to its table of contents.
- For each chapter, click it's title page to navigate there, then add a bookmark to that page.
- Once you are finished, switch to bookmark view, to see all the chapters bookmarked. This is your reading list.
- Once you are finished with a chapter, simply remove its bookmark.
This also works really well if the title is displayed in a large font on the page, since then you can easily see the title of each chapter when you are viewing all your bookmarks. This will help you decide which chapter you want to read next.
If the PDF doesn't have a table of contents, you could still navigate to each chapter's page, and follow the same steps above. It will just require more initial work.