Further to Jonathan-Joe's post, if you're determined to go via Waterloo, here are your directions:
From the Underground station, ignore all signs to the exits. Instead, follow the signs to the mainline station. When you reach the concourse (with the platforms behind you) seek out the exit at the very far left. That will take you onto a footbridge which passes over a service road and then a 'proper' road.
When you come to the end of the footbridge you need to turn right, but the steps only take you down to the left. So, at the foot of the steps, double back and pass under the footbridge.
You'll see a railway viaduct ahead. Bear left, keeping the viaduct on your right. From there, simply keep going forwards (including going up the steps you'll see in your path). You'll eventually come out by the Royal Festival Hall, onto the Southbank Centre terrace. Turn left and you'll find the London Eye ahead of you.
Chris