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.
Ubee. You take the pre amp outputs and plug those into the cross over. Then you take the bass outputs from the crossover and plug those into the subwoofers and you take the high frequency outputs from the crossover and plug those into the amplifier input on your integrated. 
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You can't use the pre out and amp direct at the same time on this integrated when the power amp direct is turned on the pre amp out is turned off.
Interestingly that was the part I was trying to figure out in the last hour. I guess this is how it works. My amp got L/R preout and L/R power amp direct.

L preout -- y adapter -- #1 crossover -- L power amp direct
                                 -- Sub (full range)
R preout -- #2 crossover  -- R power amp direct
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.