I'm refering to the properties of a reference. If I select the dll reference then i see a property called isolated. If I set it to true it allows me to reference a "local" copy of the dll without registering it and without affecting any other installation. I found out about all this from Skype where they said using isolated was "best practice".
you can also set the reference to match a specific version in your project and fail if its not found, that doesn't require anything with the manifest just ticking a checkbox