If your subwoofers are THAT different from the factory then there's a serious QC issue. Given the same signal any differences in the subs should be transparent assuming the box was made correctly. Seriously, the differences should amount to maybe tenths of a difference in T/S parameters. Shared chamber vs. independent chambers won't change your subs response all things presumed "proper"...that INCLUDES install.

So maybe I'm an ass but I'm with Matt on this one.