Notes-iPhone, Notes-Mail and Sync
While I do not have all of the answers, I would like to provide some information - based on experience.
First, it is necessary to clear up some confusion.
On the iPhone there is an app called Notes. I will refer to this as Notes(iPhone/app).
On the iPhone there is a Folder in Mail called Notes. I will refer to this as Notes(iPhone/Mail).
On the Mac there is a category in Mail, within Reminders called Notes. I will refer to this as Notes(Mac/Mail).
1. In order to sync Notes(iPhone/app) with your Mac you must connect via USB. There is no wireless/MobileMe way to sync.
2. If you create a Note in Notes(iPhone/app) and then sync via USB with your Mac, the Note will appear in Mail, in the Reminders category, in the On My Mac folder.
3. If you create a Note on your Mac from Mail, in the name@me.com folder in Reminders, it will automatically show up on your iPhone in the Mail app in Notes(iPhone/Mail) but it will not show up in the iPhone app Notes(iPhone/app).
4. If you sync via USB, the Note you created in 3. will show up in the iPhone app Notes(iPhone/app).
Hope this helps.
MacBook Pro, Mac OS X (10.6.1)