Do nothing with the subs barring level and crossover, let the dspeaker handle all your boomy bass issues if there are any , it will do so.
Use the sub in a corner or against a wall , you want the Dspeaker to cut (it wont boost) and in corners or against walls , the sub will have more LF energy due to room gain and will allow the Dspeaker to do a more effective job.
The Dspeaker , depending how you set it up , will see subs and speakers as a whole system , this is what you want , ie use it as close to the digital source as possible.