Formatting woes

I’m having a hard time with my formatting. My mobi file ended up switching all my italics to underlining etc
I’d like to try draft 2 Digital auto-formatter, but not sure how to get the raw manuscript up, whether to pre format it to .doc etc or if there is a better way.
How do you get your manuscripts formatted tidily across platforms? (I normally do a .mobi for Kindle and an .epub for other platforms)