My RF3IIs sound better set to "small," and I let the quality subwoofer(s) do the work. Your Velodyne sub should provide all of the bass you will ever need, and if not, you could always double up on subs (or go the "cylinder" route).
A caveat: I believe some Klipsch models do sound better set to "large" so there are some exceptions. For example,
KLF-C7: set to "large." The final judges will be your own ears.
Harmon Kardon AVR 525 (great brand with Klipschs)
Mains: RF3II
Center: RC35
Surrounds: RS35
Rear: KLF-C7
Front Sub: HSU VTF-2
Rear Sub: SVS 20-39PCi
Sony CD Changer C69 ES
Toshiba DVD
Magnavox 36" TV