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.
Thanks mijostyn. I found a product, FMOD Crossover which looks to me a worthy trying.  https://www.amazon.com/gp/product/B0006N41KG/ref=ask_ql_qh_dp_hza
Will it work this way?

I run a y cable out of the R and L pre amp out with one side of y to subwoofer then other end of y through the filter plugged back to amp in which filters the signal to the main speakers.
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That will work. You will need two y adapters, one for each channel. I have used this Hsu high pass filter with great results. Take a look at the owners guide and it shows how to hook up a high pass filter!!
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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