My understanding is you would only want to use the speaker level inputs in a 2 channel set up.
EDIT: Actually, if you set you mains to large and the cc and surrounds to small and no on the sub, all the bass info from those channels should be routed to the mains but why bother if your receiver has an lfe out and your sub has an lfe/line level in.
EDIT: Actually, if you set you mains to large and the cc and surrounds to small and no on the sub, all the bass info from those channels should be routed to the mains but why bother if your receiver has an lfe out and your sub has an lfe/line level in.