Bootstrap is designed to be a lightweight wrapper for protobuild.exe, allowing you to update the version of protobuild in your repository without needing to deal with storing and merging lots of binary blobs in your repository.
Place Bootstrap's protobuild.exe in the root of your repository, much like you would a normal Protobuild instalation. Then, simply set the ProtobuildVersion value of your Module.xml to the desired version hash.
To update Protobuild, simply bump the hash. No replacing of binary files required!