It’s not a case of manuscrpt styles.
For the paperback, print-on-demand version, do whatever you want.
To create your Kindle file, you will always be working from your source text file or files. The Kindle file doesn’t import or use manuscript styles. You import ‘raw’ text and have to use Kindle’s own paragraph styles.
To create your Kindle file, you have three options.
(1) Use the software tool that Amazon provides. It works from your text file to generate a Kindle file. Downside: (a) it doesn’t work very well. (b) It doesn’t generate a .mobi file that you can do with as you wish. It generates a file, in Amazon’s own proprietary format, that only Amazon can ‘unlock’, so to speak. Sure, you can upload it to KDP and thus make your book available in Kindle form on that platform, but you can’t do anything else with it.
(2) Send your source text to an agency that prepares the Kindle file for you. Doesn’t cost that much and some of them are really good and fast.
(3) Learn how to make your own Kindle files, working from your source text file(s), using a tool such as Calibre. I’ve been through this learning curve and, well, it’s a little tough but you can do it, provided you have access to someone else who also knows how to do it.
If you want any more help, my website is www.ianrowland.com where there’s a big section on self-publishing.