I have never figured out what to do about notes. If you add notes in FTM they all seem to not be viewable by anyone on Ancestry.com unless you give them editor status. I don't do that for most of the people who I share my database.
At one time I was putting in extractions (i.e. obituaries, vital records, county histories, etc) as notes but no one could see them. I put them in as comments on Ancestry tree but comments don't seem to download to FTM.
So I guess if you want a note that is not viewed online by others you can put note anywhere because I think they all go into the note section online. If you want notes in both FTM and Ancestry.com and viewed by others, the only way I have figured out is to make it a text media file.
I sure hope someone comes along with a better understanding than I have on what to do with notes.