I convert from epub all the time to mobi. The only problems I have is margins and indentation sometimes are off but there is a ignore margin option box you can check to fix it and if that doesn't work you can explode the epub and edit the style sheet directly.
For indentation I just add an override style in the Extra CSS box. That usually fixes it right up.
As for Chapter detection every epub is different. Sometimes the default regex will work and sometimes you have to look at the way the book is coded to get the right regex. You can view the ebook's code quick and easy in Search and Replace. Sometimes Heuristics Processing will fix it all right up for you but It's really trial and error most of the time.
I had a few epubs that I had to remove all font tags to because it keeps you from being able to resize the font on the Kindle. I would really love automatic option for this because it's not till I get it on the Kindle do I notice an issue.
Batch converting is something I don't recommend because each book is different and results will vary.