With the speakers set to large the receiver doesn't cross over to the subwoofer. Set like this the subwoofer will only play the LFE track (the .1 in 5.1) from multi channel sources, leaving the speakers to play all parts of the audio that is designated for them.
When you set them to small the receiver sends everything below a set frequency to the subwoofer. If you want to use the subwoofer with 2 channel sources, or give the mains a little bit of help with the bass you need to set the speakers to small (recommended) or turn on the "double bass" (I don't think that's what pioneer calls this option, but it will be something like that) option that will send bass to both the speakers set to large AND the subwoofer.