Do you edit it yourself or do you work with an editor? Word has the advantage of very good editing tools. But since you already made the epub, that would mean extra effort. I would ordinary expect to first using word for the word processing and editing power of it and then making the epub.
If you do the editing yourself (or with a printout), why don't you just read the epub (or mobi)? Most readers have annotation functions you could use. It would be exactly as much work as working with a print-out (if we are talking copy-editing. For heavy editing I think using word would work better).
Finally if you prefer a print copy, I think you can print the epub directly from the calibre viewer. Or you can use prince or calibre to produce a pdf and print that.
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