If you had done a full system restore from Time Machine, it would have been done automatically. But 3rd-party cloning apps don't leave a "trail" so Time Machine can figure out that the new drive has all the old stuff on it.
Effective with Lion, there is a way to "associate" the new drive with the backups of the old one, but it requires the use of Terminal. See #B6 in Time Machine - Troubleshooting. As noted though, this only works on directly-connected backup drives, not backups made over a network.