Just the for the record.. I am right-handed. I wrote my first reply at 4:30am.. so I was a bit tired.. hehe.. Basically.. yeh, I use my left foot.. I had exactly the same problem that you did when I first got it.. I was like, "Huh? I don't understand.." and I couldn't get it at all. I also have a Jim Dunlop Cry Baby. Like most of these type of things the signal chain I use is from guitar to wah-pedal to amp/computer. Using the wah after another fx pedal, such as distortion doesn't appear to work as well for my purposes.. though it depends on what sound you want..

It's not the same thing as tapping your foot in time with the music, which I would normally do with my right foot.. tapping a foot is generally quite a passive thing unless you are also actively counting the beats.. playing wah is generally a very active thing.. may be that could help in finding the science behind it.. but really.. I think it's more of an art than a science..