Hey Aaron,
This is a good question. The answer is that you don't need to use any tricks. You can use the .NET 3.0 version of the AutomaticUpdater now and use the .NET 4.0 version of the AutomaticUpdater when you switch your program to .NET 4.0. You don't need to do anything special. wyBuild is smart enough to know the files are different and it will generate the patch to go from one version of your software to the next.
I'm not sure if you've read it yet, but the step-by-step walkthrough is a good place to start.