You control the bottom row. You must make it match the top row. Simple.
There are four different game modes – Wave, Colour, Data and Audio – but they're all fundamentally the same: you have to use the arrow keys to modify the bottom row so it matches the top row. In Audio mode, you must modify the second beep in the pair to match the first.
When you think you're close enough, press space and the game will calculate the difference between your wave and the original. This will be added to your previous scores and averaged. If you match the top wave exactly, you will be told immediately.