I think it would depend on whether your fronts are full range speakers. If you set it to Full I assume bass is directed to the bass drivers, which would give you in essence 2 subwoofer bass. With extra bass, if you like the sound of extra bass, then I would use that too. If however your fronts are small speakers, then I think you would get better mid-range if you set the speakers to small, and use extra bass, which would direct the bass to the subwoofer.
Another trick you can try is if you have Full range fronts, you can set speakers to small. This can give you better mid-range upper bass, and you can still use extra bass which will send lower frequencies to your sub. It also takes the bass work load off the amp, so you can crank it louder.
That's the beauty of the SP3, I have an SP2, which gives you options to customize sound to your liking. Another trick is you can change distances for speakers, which can give you a more forward sound or laid back sound.
Currently though I'm into 4 channel stereo with my SP2.