I have loaded documents that have thousands of pages. As outlined above if you know which page you need to access you can uses the page bar.
Links in pdf's can be used. I modded a document of mine with a couple of links and it will work. This can be a time consuming and cumbersome process using Acrobat (I use 6, I don't know if the newer versions are easier).
Currently bookmarks do not function. See jaed's post on his program that will develop a table of links from the bookmarks in pdf files as a stop gap till iRex integrates bookmark support. I will be trying jaed's program when I get a chance.
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