How to calibrate dual subwoofers?

I have two subwoofers, Polk Audio PSW350 & Hsu VFT2. Each sub is placed next to each main speaker. I use the Y-splitter from the subwoofer output of the Yamaha AVR (used as pre/pro). I use the Radioshack SPL meter to calibrate. If I measure the subwoofers against the Left main speaker, there would be no way to tell which subwoofer is louder than other. When I watch movies, I could feel that the the left-hand-side sub louder than the right-hand-side sub. Does any one have any suggestion on how to make the left and right subwoofers to produce the same volume? Any advice or help will be greatly appreciated.