You can use the velodyne SMS-1 to equalize the subwoofer properly. If you are hearing the subwoofer, then it is not integrated properly.
Some things you want to make sure you have set properly when dialing in the sub is volume and phase. You should be able to hear the subwoofer when you crank up the volume of the sub separately for added kick; for parties or just to jam out. You should never hear the sub when it is on and you are playing your music. If you do, then addressing subwoofer placement should be considered. I have my sub aligned on the same plain as my speakers, firing from right to left.
For an example, I was playing some music the other night and was amazed at how deep the bass was in this song and how punchy the bass was, Children of Sanchez (LP edition), Chuck Mangione, and when the tom toms struck, man, I was in awe, the bass was deep and articulate, I never perceieved the bass originating from the sub. I switched the sub off, and did not perceive a loss of localized bass, it just seemed that the system could not reach deeply into the subsonics, but the all tube based unit, with KT120's, still shook my room, driving B&W N800's, without the sub. Yes, some of that is system dependant, but, I integrated my sub using the SMS-1 and that device has worked miracles in regards to integrating the sub. I use an ASW850 sub with my system.
Anyone should be able to integrate a sub properly given time and the proper tools. Even without an outboard EQ, setting the volume, and setting the phase 180 out, may make a big difference.