I've done some testing of various Bluetooth headsets for work... and of all of them, only one claimed to be able to handle call waiting. I couldn't get it to work.

I don't think it's very well-supported in the current version of the Bluetooth standard, especially using the headset or handsfree profile. I think handsfree might add some rudimentary support for call-waiting, but I've yet to see a good implementation of it, including headsets from Bluespoon, Bluetake, Logitech, Sony Ericsson, SouthWing, and a few others.

And since the Prius is just a really, really expensive headset, as far as your phone is concerned, I don't think there's much that can be done. Not sure if BT 1.2 does a better job of it, much less if the Bluetooth stack in the car can be updated in the future to 1.2, should that be the case.