Joshua
> Any advice on how might we best accomplish this with InDesign?
What Dick said.
ID is much more expensive than MSW because it is much much more robust in doing layouts (and it has a pretty good word processor within it).
Dick and I just participated in a discussion on another list about almost exactly what you are facing, namely, handling endnotes and footnotes in MSW and ID. ID can do it if the two note streams are separated in MSW, that is, one is a sequence of endnotes and one is of footnotes. The other factor is that the two sets of notes use different callout tokens, typically arabic numbers for endnotes and symbols for footnotes. If you set up the endnotes in MSW to use arabic numbers, then you can use ID's Document Footnotes feature to assign symbols to the footnotes.
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Michael Brady