Reminds me of reading the print version of Infinite Jest by David Foster Wallace, where you needed one bookmark for the novel and another for the endnotes, which made up like 20% of the book. Hopefully e-readers make that easier now.
Depends on the reader I suppose. But in my expirances, its much much worse. You see, in a book you can quickly flip back and forth between pages. Moving bookmarks takes no effort. On a ereader you have to pick your page via a menu, go go your book marks via different menu. Delete bookmark via menu
Menu menu menu click click click its awful.
Got a book with a map at the front? Well you better memorize it because its not worth the effort to flip back and forth when ever some location comes up.
On the phone I think I would use two e-reader apps and just switch them. :-D
This is all nice and well, until your footnotes are half a page of explanation that was impossible to fit in the text directly.