Well, I'd add new project configurations, and set the build type for each configuration, along with the output directory. So you might have "Debug x86" and "Debug x64" project configurations, with output directories of "bin\DebugX86" and "bin\DebugX64" for example.
That's a change that can even be done within Visual Studio, unlike most of the project file hacks I perpetrate :)
That won't build configurations with a single "build project" button press, but:
- You could add a post-build step for one configuration to build the other
- If this is only relevant when you build the Wix installer, I'd just script the building of that to first build both configurations
Another Visual Studio feature you should look at is the "Batch Build" option. Unfortunately it doesn't look like there's a way of saving a batch build to perform it multiple times easily :(