If the sound is similar at the same volume levels when using either amp, the problem is the subwoofer. If the sound is poor out of the dedicated at the same volume levels, the problem is the subwoofer amp.
Location and phase are also issues, but I assume those are the same with both amps.
Also keep in mind, depending on how the subwoofer is constructed, if you place a cinder block or two on top (wrapped in a towel or some material), it will tighten up the sound quite a bit. Cinder blocks only cost a few dollars to try it.