The AutomaticUpdater is at version 2.6.11.2. Like I've said before, we only update the version number of a component if we've made a change to it. The current version numbers (as of January 26th, 2011) are:
wyBuild 2.6.11.3AutomaticUpdater 2.6.11.2wyUpdate 2.6.11.3
But to answer your question in more general terms, after you've updated wyBuild, to make sure you're using the latest AutomaticUpdater simply rebuild your app. Visual Studio will then copy the latest copy of the AutomaticUpdater into your app's build folder.