I was part of the Nielsen family and everything is automated.
They hooked up their detectors inside my ReplayTV boxes, which I wasn't all too happy about, but in the end, they didn't break anything. But whenever you watch your TV, whether it is through a computer feed, DVR feed, or live TV, you are supposed to indicate through a remote who is watching. That way they get demographics on who is watching. They didn't tell us how they analyzed the data, though. We often watched shows which were very old because we had never gotten around to watching them yet. So in the end, they didn't care about what shows you recorded (because they cannot get demographics on who is recording) but they care about what you watch, whether recorded or not.