IDCS1? ID2? Been there, done that. But don't rush into this. Even if you have healthy footnotes in Word, InDesign has a nasty habit of "disappearing" a few on importing the Word file. It doesn't happen with every file, but it happens more often than it should. You might want to consider using separate files for body text and notes during editing to ensure you only have to cut-and-paste once. Or maybe IDCS6, due imminently, will finally handle footnotes reliably.
Then there's scripting. You could see whether Peter Kahrel's tools might help. Marc Autret also wrote a couple of scripts that can move footnotes into the body of the text and then back out again into ID footnotes.
Our TextExporter has some support for exporting footnotes: it can 'inject' them into the main text, jammed between two 'markers'. Not quite the same as 'real' footnotes, but better than losing them all together. Don't get your hopes up for round-tripping though! Unless it's a very specific workflow, ID -> Word -> ID is not really practically workable.