I've done first step with bookmarks in all-in-one ipdf. It's working now.
1) You can add bookmark for page by pressing icon which following by "pan" icon.
2) You can view and navigate bookmarks by pressing "sort" icon.
3) Bookmarks are stored in manifest.
4) Now it is possible to add just 10 bookmarks (I need to display them in several pages)
What I plane to do:
1) Add comments to bookmark
2) Devide bookmark in to pages
3) More nice design of bookmarks view
4) Pre-load of bookmarked pages
Please, if somebody will try to use it - be careful. I am not sure, that it works correct, so using of this ipdf is on your responsibility.
With best regards,
Moderator Edit: For an easy installer to use with firmware 2.11 see this post