I wish you could do this. It would make iDisk perfect, as I could sync folders on my hard drive and my idisk with no initiation on my part. The only way to achieve this is to have my folders 'live' in the idisk.
I don't get it, why don't you use the backup.app software which is provided for free in MobileMe. You can determine which of your HD folders should be sync'd to the iDisk and also when they should be sync'd