Here's some instructions for you guys if you have an existing MobileMe account that they want moved over to iCloud but have a separate login for their iTunes and App store Apple ID. It took awhile but I have everything running correctly.
1. Copy everything from your iDisk to your computer.: The service stops sometime next year but now would be a good time to do it. You could switch over to Dropbox and retain some functionality.
2. Log into MobileMe.com: And walk through the transition procedure they have. It's easy to use and very cool looking. This allows you to keep your
name@me.com email address.
3. Setup your iCloud account on your device: DO NOT use your AppleID if it's different than your MobileMe login. My Apple ID was a gmail account.
4. Select the Store Preference on your iOS device: Put your other Apple ID in here. In my case it was my gmail Apple ID.
You should now be able to have all the features of iCloud while still retaining your App Store and Music account. I've bought applications and it syncs seamlessly and doesn't ask me for any input.