Webpack handles sourcemaps, and one of us, gajus, has already integrated it. Prepack should be just another stage in the build pipeline.
Having said that, there appears to be a sourceMaps flag in the Prepack source: https://github.com/facebook/prepack/blob/57cc59c07d164e4827c...
I will be attempting to use this as a simple black box, relying on Webpack for features that are only tangentially related to this new optimization stage in my build stack.