I'm having a problem following that you said up front, but these are your options from the equipment you listed.
You can feed the speaker level output of that little amp into the subwoofer speaker level inputs and connect the speakers to the speaker level output of the subwoofer.
If you feed a line level input into that subwoofer, you'll get nothing out of the speaker level inputs. They only contain amplification for the subwoofer, not any other speakers. They only pass through what's fed into them.
I don't suggest connecting two pairs of speakers to either the little amp or the subwoofer speaker outputs. I don't see any mention of how well it would handle a four ohm load. I'd use a separate amp for each set of speakers.