I just go to the market and see if it needs an update there. The Cleanrom I installed already had the latest. Just checked now, and it still does. Are you sure a newer version than what you have is available? Market have an update?
Like i said, I've installed the one that is included in the one click rooting method, I've installed the one from market, and I've installed the zip file from the official download. All of these seem to work fine until it comes time to update the bin.