Here is a quick way to get a fairly good rough set-up.
Start with the PEQ gain set to minimum (off). Set the crossover frequency to about 120 - 150hz. Set the gain slightly higher than normal. Play some music with deep bass and, while sitting in the listening position, have someone adjust the crossover phase until you hear the highest level of output from the sub. The goal here is to get the phase set correctly. The sub will sound the loudest when there is a minimum of out-of-phase cancellation in the overlapping frequency range. The phase setting should now be set roughly correctly.
Then set the crossover frequency to about 50hz (to cross with the SongTowers) and, while music is playing, turn the gain down very slowly until the sub stops calling attention to itself. Once you have the gain set properly, you should not notice the sub except for the fact that your system now plays quite a bit deeper than before. If you notice the sub, the gain is probably set too high.
While this is not a very sophisticated setup procedure, it should get you in the ballpark in fairly short order.
Establishing more precise settings and using the PEQ function appropriately will require measurements. THUB and Nuance have posted quite a bit on this topic and you can search for their explanations.
I hope this helps.
- Jim