WebGrease supports two modes: runtime and buildtime.
Runtime mode is used by ASP.NET during bundling and minifying. In this mode, WebGrease DLLs are called during the run time of the web site.
Buildtime mode (or command line mode) is used when WG.EXE is called from command line or from build process.
WebGrease manifests is the feature that is only available for build time or for running WG.EXE from command line. These manifest files provide the way for user to add the additional configuration parameters for WebGrease (such as "GlobalsToIgnore").
Unfortunately, WG manifests are not available for runtime. So, if you are minifying from ASP.NET, you will not be able to use them.