I think for the new Onkyos (mine is the 600) if you are using something with a dedicated LFE track you are fine, the sub will come through since there is a specific track for the sub. However if its just a CD or its compressed equivalent it will only be sent to the L/R speakers. The amp won't reroute any audio from their intended channels.

I can't comment on the 3007, its a little too nice for my price range at the moment, so I haven't done any research on it. Damn student loans.