Wiring question : amp-sub-speakers


I am pretty new to audio world and am looking for an advice regarding wiring Denon PMA 2000 IVR integrated amp, Polk PSW 550 sub and JBL studio 530 speakers. Current wiring is, Amp to JBL using the main binding post and Amp to Sub using preout. It sounds great up to certain volume level and JBL 5" woofer starts over-excursion, aka bottoming out, at a higher volume(knob 11 o’clock & >90 decibel) to fast tempo low frequency sound like drum kicks. I am not sure how to improve this situation. Sub manual suggest "Speaker-level" connections, i.e., Amp to Sub and Sub to JBL. Is it connection issue, JBL issue, or Amp issue? Thanks in advance.
ubee67
Page 6 of the manual on the Denon PMA2000 IVR, number 16 Pre Out terminals (PRE OUT) , under NOTE, No signal is output when selecting power amp direct terminal. You CAN'T  USE  the PRE OUT  and AMP DIRECT at the same time. 
They are just capacitors. They will roll of the bass at 6 dB/oct. You would hook them up in series with your main speakers. The value depends on the impedance of your speaker at the cross over point. You can find charts on the net which will give you the right value, somewhere between 200 and 300 mfd. As im said go to Parts Express and order two.