Generally, it is different. In home audio, the subwoofer is a discrete channel, usually with its own separate speaker wire. That's what "5.1" means. 5 discrete audio channels going to 5 full-range speakers, plus a discrete subwoofer channel.

Dignan,

Any system where the subwoofer appears to be daisy-chained with a pass through to the other speakers means that either it wasn't wired for true multi-channel operation in the first place, or that the subwoofer has some kind of internal smarts that is doing the multi channel decoding itself.

This latter case, where the subwoofer has its own internal smarts and does the channel separating itself, is fairly common, so check to see if that's the case here.