How do you get eye diagrams?
First you have to set persistence on your scope. Normal persistence will show newer data over the previous, while older data fades at each scan. Infinite persistence also displays new data over the older, but the older doesn't fade, so that you can have literally thousands of images on top of each other.
There are two ways to create eye diagrams. One uses the external trigger where you connect the clock signal. Upon a clock pulse data can be high or low, so over time you'll see both pulses on top of each other.
If you don't have a separate clock signal the data itself is used to trigger the scope. If you look at a Manchester coded signal you'll see that pulses aren't always equally spaced. If you have 01 and trigger on the 0 the second bit will show low and then high, but when you have 00 the second bit will show a high followed by a low, the transition (which is actually the clock) will be at the same place.
So even when you trigger on a low to high signal some time later you may have different levels on different times.