I take it you mean like a 2GB or 4GB flash drive and not a hdd right?
I've never really thought about partitioning a flash drive... its pretty small as is. The only problem I forsee is the controller for the flashdrive, it may not be able to handle more then one partition. I'd try it out on my flash drive, but I don't want to xfer all the info off this 4G'r on this USB 1.1 PC.