Instead of linked indices, it is often better to use the built-in search function that is available on most devices.  By the time of this writing, it might be available on every device.

When you use linked indexes, the only thing that the page numbers can link to is the page where the text used to be in your Word file.  Or in your PDF file.  In the eBook, when a user clicks that, it might be several “screens" away from where the word is actually used.  (This is due to how Word sets the index links when you generate them automatically).  You can see how this could frustrate your reader.  This is why we recommend not using linked indexes.  If you want them, we are happy to provide them, but please give the matter some thought.  Remember that you want your reader to have the best possible experience.  Below you can, on the left, see a screenshot of a search on an iPad, and on the right, the result of clicking one of those search results.  Click the images to enlarge in a lightbox.  

LJ Sellers' The Baby Thief, showing a word highlighted, that the user wants to search for in the book.
LJ Sellers' The Baby Thief, showing a word highlighted, that the user wants to search for in the book.

 

For some books with only a few notes, a small bracketed annotation--i.e.., [1] inserted in the sentence might be best.

Thanks to L.J. Sellers, a Booknook.Biz client, who now has a major publishing deal with Amazon, for letting us use screenshots from her bestselling title, "The Baby Thief" on an iPad for this FAQ article.  You can read more about L.J. Sellers at Amazon by clicking here. 

The book now displays the search results, which you can go to with a tap--and then back to the page you were reading. Pretty cool, eh?
The book now displays the search results, which you can go to with a tap--and then back to the page you were reading. Pretty cool, eh?