Word can work just fine. I create books with the word generated toc, linked endnotes, etc. and it works like a champ. I have found a couple things that need to be done though.
First, always use styles for everything.
Save as filtered web page.
In Sigil, delete all the lines in the style section of the html document.
Create a css file with all the styles that you used in the word document.
Link that style sheet in the html.
You are good to go!
I do some additional cleanup, like a search and replace to change <p class="MsoNormal"> to just <p>.