My suggestion would be to edit it in MS Word (OpenOffice, etc will do) and use the styles feature to make the headings, etc. For example, a chapter title might use Heading 2, a topic within the chapter might use Heading 3, and so on. It's extremely important to use styles in chapters, etc., because that will allow it to be easily exported to HTML, which can then be easily converted to Help format with the table of contents automatically generated.
I don't know how well linking within the document would work, but it seems to work pretty well.
All of this assumes that you'll be doing this in Help format, which would be for Bw. I have a lot of stuff in Logos, but it seems to be a little more difficult to get the formatting correct, and even then, the font kerning is messed up. Maybe that's just me... Either way, you'd probably still have to go through the Word styling step.
"Contend earnestly for the faith that was once for all delivered to the saints." Jude 3 (ESV)