Eric Charran has written a nice post on dealing with ClickOnce manifests in Team Build.

Building a ClickOnce Manifest File with Team Foundation Services Team Build

Issue:

When building a ClickOnce application using Team Foundation Build Services, the goal is to modify the details contained within the .application deployment manifest file to conform to desired settings segregated by build type.  This would allow Build Masters and Release Managers to build the application using different build types within Team Foundation Server and have the drops for those builds take on different deployment profiles.  For example, the deployment URL for a specific debug drop would be different than its production companion.  In order to change this, the information within the project can be altered so that the build process honors the settings, but this approach is not maintainable (i.e., every time the project is build, a developer has to manually edit the .csproj or .vbproj’s ClickOnce deployment settings).