Firstly, I really like how the phyisical connection of being "clipped in" makes me feel like the bike and I are one machine.
Regarding pedaling, I don't pull up on the pedals when riding but I definitely do the foot scrape along the bottom of the pedaling arc.
Also, when I get that old twinge in my right knee, focusing on perfectly smooth pedaling with plenty of bottom scrape usually sets things right. Cant really do that with flat pedals.