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Unfortunately, I haven't seen any way to prevent iCal on your Mac from syncing an extra copy of the calendar over. If you subscribe your Mac to the DueSoon file, you'll get double-notifications on the phone.

Once we can get the calendar sync code rolled into the Mac app and released, your Mac will be able to do the calendar updating when it Syncs; at that point MobileMe-synced version of the calendar will still do the job and notify you. Sorry for the inconvenience this causes in the meantime.