MacOS – Why did the desktop and documents suddenly get renamed “Desktop – Local” and “Documents – Local”

From what I read, you actually are almost there. It looks like your problem may be how the folders are done (as in, locally or on the server).

As you said in your answer, you copy the emails to local folders, so therefore they would never be on your phone. And with iCloud's limited rules (in the cloud), as you note, you cant really make a sound or do much with them either.

As long as your Mac is always running (to run the rules), you really would only need to update your local mail rules to put the emails in the servers folders. This way if you are at your computer, you would hear the audio cues, as well as have the mail filtered. If you step away, as long as your Mac could still process the mail, it will copy the emails to the correct server folders, and be available.

On your Mac now, you should see two inboxes, iCloud and 'On My Mac'. Make sure folders exist under the iCloud account for where these messages should go. Then update your rules to point to the iCloud account folders, versus those on your mac.

The only thing you may see from this is some messages will be in your inbox for a very short period of time (before your Mac runs its rules), versus iClouds server side rules that process mail before its delivered.

You can disable iCloud on iWork by going to the Settings app, and scroll down to the install apps settings, you will find each iWork app has it's own section, Pages, Numbers and Keynote.

In each iWork app's settings there is an option "Use iCloud". Turn this to off, and keep the Documents and Data in the iCloud menu on.

For Mac, the iWork apps do not support iCloud Document Sync. (If you enable sync on iOS, the files created on iOS will download into your library, you can't open them however, and you are unable to upload to iCloud in iWork)

In Mountain Lion they will, but it appears that iCloud Doc sync integration will be at the OS Level, rather than iWork app level. Instead being more like DropBox* where you have an area (I say area, because it's not a folder, but it's quite similar to one) for iCloud.

*Although this area only seems to appear in Open/Save Dialogs, and will only show files that are registered to the App.