Go up into the mainline station. With your back to the platforms (as if you'd just got off a mainline train), take the exit at the far left hand end of the concourse.
Personally, I wouldn't both travelling to Waterloo (unless I was arriving in London at a station, such as Euston, which has a direct tube line to Waterloo). If you'll be arriving in London at a mainline station served by the Circle Line, simply travel to Embankment. When you leave Embankment station, you can see the London Eye just across the river. There's a footbridge, right alongside Embankment station, which gets you there with only a very short walk.
Chris