Notes not syncing to and from iCloud from OS X Yosemite
From what I've seen from Apps like Notes, Numbers, and Pages... They're now acting as usual apps which looks for "filesystem" files. i.e. something on the local drive.

When you fire up an iCloud enabled app, then need to open a document, in your Favourites is "iCloud Drive" and now things are stored under there, under folders which correspond to their apps i.e. Numbers, Pages etc...

As to the syncing.. You needn't worry about this. Apple handles this.. Sadly, if you're looking to move directly over from App 1 on Device 1 to App 1 on Device 2 in 1 second, it won't happen.

edit

To resolve this, what I've done in the past is delete the container that the app in question lives in and start again.

e.g. in your case.. notes lives in: ~/Library/Containers/com.apple.Notes

Problem is, when you do this, you probably will lose the notes you have... The ones which are already in iCloud will resend back down to the Mac you deleted the notes Container from.

Do note that after you do this, it's HIGHLY advised that you do a  "repair permissions" on the drive so the sandbox permissions/ACL's are reset.