In our workflow, once a book is in ID it never goes back to Word; all of our updates and other maintenance are done in ID. If it's just you working on the material, you'll just need to pick which tool you think you are most productive in for writing. Since your project is a manual, page layout is going to be more important than it would be for something like fiction…I'd be tempted to author in ID, especially if you have a lot of graphics to place, callouts, sidebars, and the like. A disadvantage is that you can't just send off a Word file for someeone to edit…they'd need to edit in ID, or, as we sometimes do, annotate a PDF.
Regarding styles, it almost doesn't matter what the styles are in Word, since you'll be mapping them to styles in ID. During edit we just use the Word styles to tag elements of the text, not caring what the Word file looks like. You also have the option when you import the file into ID to leave the Word styles in place and import them rather than mapping them to ID styles, so if you use logical Word styles such as Chapter Title, Caption, and so on, they would appear as new styles in ID, which you could edit. I think a common error that folks using both Word and ID make is to spend tons of time trying to get the pages to look right in Word…they aren't going to look that way in ID without a lot of effort.
If you are committed to keeping the Word and ID content in sync, my advice would be to treat the Word file as unformatted but styled source, and do double edits, especially if the layout is complex.
Perry
KidPub Press