You can only have one version of TypeMock active at any given time. What that means is if you have two different projects that rely on two different versions of TypeMock, you can use the auto-deploy feature to switch which version is active at any given time, but you can't run both simultaneously.
This is more of an issue in a build server environment where you might want to build the two projects in a multi-threaded format so they run at the same time - in this case, you can't. You'd need to figure out how to serialize the builds of the two projects so the version of TypeMock that's registered isn't switched during the point at which it's being used.
