Thanks guys. I think the idea to tell the receiver I have no sub, that the front speakers are "small," and the rears are "large" is probably my best bet. Thanks, Dan. Clearly this is far from ideal, but I can't be blamed for how their installer did this initially.
I can't imagine why they did, though. Why on earth would you do that? As long as I've been familiar with home theater setups, the sub has always been discrete. It couldn't have been to save money either, as these people had a pretty nice Denon receiver, a whole-house speaker system, and amps to drive it all. Seems crazy to me that if you're going to run all those wires anyway, you'd run something to the sub separately.
Could it be because they were using an in-wall model that wouldn't be able to get power to, like Cris said? I agree that the sub will probably be less than satisfactory.
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Matt