The 3206MSO, and Picoscope 6 software, are not designed for creating eye diagrams from a repetitive signal. When switching to ETS you are only able to select a rising, or a falling edge trigger, which would not work as you require both edges to create the eye.
For true eye diagram analysis you would need to look at our sampling scopes http://www.picotech.com/picoscope9000.html
. However if you are looking for a general indication of an eye you could run the 3206MSO in Persistence mode with an advanced trigger set for both rising and falling edges to create the eye. You can download the software from http://www.picotech.com/software.html
and try this out in demo mode to see if it meets your requirements.