Most of my clients supply their ms' in Word or Open Office format which I export as filtered html and then clean up in Dreamweaver which has an excellent command for removing all the junk that Word & OO introduce. Once the code is clean I convert it to xhtml then copy and paste it into a blank Sigil book. I find Sigil a pain for editing the xhtml as it is always trying to second-guess what you're trying to do and has a nasty habit of screwing up your code if it doesn't like what you're doing. However Sigil is very good at making the TOC and packaging epubs, and the validation tool is superb.
InDesign is great for laying out magazines but rubbish for making epubs.
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