The request to learn how to do InDesign book and manuscript tasks is on the increase in our workshops. The reason is, more and more scientific publications ask their authors to have copy-ready papers, and InDesign is so much more cooperative than Word when designing columns with graphics.
InDesign DOES have a footnote feature, and it's easy to use. Here are the pros and cons:
The good: Footnotes and endnotes from your Microsoft Word documents can be imported into your InDesign documents.
The bad: InDesign completely disregards your own Footnote And Endnote numbering options. Instead, it reformats footnote and endnote reference numbering to regular text.
The ugly? Decide for yourself on this one: InDesign can't convert your text to approved publication styles the way EndNote, a Word and WordPerfect plug-in does, so you'll have to style them yourself.
As I said, it's very easy to do. See this excellent tutorial by David Blatner of lynda.com:
http://www.wonderhowto.com/how-to/video/how-to-create-footnotes-using-indesign-cs3-3785/view/