"Convert" in the subject field is for Amazon to convert the book themselves. calibre already sends a MOBI which your Kindle can read without conversions, so... no need to convert.
I have never known the email
body to mess things up, and many many many many many people use calibre to email books to their Kindle.
Notes and highlights are completely different. If you've gotten that far, then your books were already sent, yes?
I don't think notes will be saved if you don't have the option in
http://amzn.com/myk set to enable syncing annotations.
I am also not sure whether Amazon supports online viewing of annotations for Personal Documents, so that may not work anyway.
I'm not really 100% positive since I don't really pay attention to
http://kindle.amazon.com 
Regardless, it involves the actions of your account once it has already received the book.