how to use notes on a PDF file in iBooks for iPad iOS 9

I have a long PDF file where I want to have a quick access to certain pages.

I marked these pages in Preview on El Capitan (10.11) and syncs the file to the iPad (iOS 9). I also rotated some pages.

When syncing to the iPad the rotated pages went back to the original position. In addition - I don't see a way to see the notes and go directly to the right page.

Bookmarks do not work for me as I cannot edit their content.