Setup your mechanical timer for the TIME OF DAY and LENGTH of TOTAL TIME ON (standard stuff, just like the old pump)
on the new pump - it automatically kicks to V3 by default, which is highest speed. For everyday skimming and running, I found I only need to run mine on ~2500 RPM for 3 hours, then I let it run for 1100 RPM for another 7 hours. Sometimes during the summer I run it for 21 hours, since electricity is cheap here, and it gets hot, so that helps thwart off the algae by keeping the water moving.
Anyway - it will default to V3, and run V3 for either the full running time (I think the default per speed is 12 hours) then it kicks down to V1. It skips right over V2.
Again, I programed V3 to 2500 RPM for 3 hours, and then V1 I kicked down to 1100 RPM but bumped it up to 18 hours. I change the total run time with the mechanical timer.
I then reprogrammed V2 to be max speed (IIRC, 3500 RPM?) but I only ever use this if I am manually vacuuming the bottom so I turn it on and off manually.