Having problem similar to geko (May 15, 2009 post). Have version 9 Pro. Setting destination for bookmarks no problem if bookmark set within upper 75% of page, but if set within bottom 25% of page, bookmark takes user to top of next page. Have tried: using set destination on right-click menu or on bookmark pane options menu; scrolling to and selecting text on line where bookmark desired (positioned at top of view window) and then creating new bookmark; and, selecting single page continuous, single page, or default page layout on properties initial view tab. If I readjust slightly upward the position where I want bookmark set, about 30% of the way from page bottom, then bookmark "takes"; as I ever so slightly readjust back downward, as the bookmark set position nears the one-quarter point again from the bottom of the page (not page margin), the bookmark jumps to the top of the next page. I had the same problem and solved it two years ago in version 8, but foolishly neglected to write down the solution. I have made note of all properties and settings I can see in the file created with version 8 and and made sure my current file has the same properties and settings, but this does not help resolve the problem.
http://www.acrobatusers.com/tutorials/2008/10/auto_bookmark_creation
You might want to consider breaking up the large PDF so it can be packaged or used in a portfolio.
Here'd one more tutorial to check out.
http://www.adobe.com/designcenter/acrobat/articles/acr7sdbookmarks/acr7sdbookmarks.pdf
Hope this helps.
My favorite quote - "Success is the ability to go from one failure to another with no loss of enthusiasm.