I’ve published a number of anthologies thanks to Kindle’s free self-publishing service.
It’s a great system, and you can design your own front cover and upload your work and hey presto you are published.
However, the Kindle system does expect Word files to be properly formatted for e-reading otherwise you get serious problems with indents flying all over the place.
Using Word STYLE set up a default style for Paragraphs to be set at First Line Indent, and also check the box so that no extra spaces are included after a paragraph.
Don’t forget to set up hyperlinks from your Contents to your Chapters.
For Kindle don’t have a footer, you don’t have page numbers in Kindle.
If you want to self publish in paperback save your finished book under a new name and in this copy, add a footer with page numbers.
Upload your file to createspace, chose a book size, and go through setting up. The system will make what changes to layout are necessary and offer you a revised file to download. Do so and use that as your file from now on.
Your file should now mirror the finished book but do check by uploading again. Go through publication till you get past its page formatting check and you reach preview. It is only at this point that you know the proper look and pagination for your finished book.
Make a note of the page numbers you want to reference in your Contents. Go back to your Word doc and update contents page with page numbers. You can do this manually or though Word TOC. Save, then reload your doc to createspace and you should see your final completed masterpiece.