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.
I tried what millercarbon suggested - reduce bass down from amp and increase bass up at Sub. It worked but I do not like the sound quality. Eventually I hooked up speakers through Sub speaker level out, aka high level out. It does not fix bottoming out issue but, instead I feel Sub and speakers timings are in sync and it appears to be recommended method for 2channel stereo setup.
ubee, It does not matter what speakers you have or get. In order to match up a subwoofer correctly the crossover has to have a high pass filter that rolls off the bass to the satellite speakers. Then you will not have a problem overloading them. This business of just putting the subwoofer on a low pass filter and doing nothing with the satellites is a cheap silly solution that as you have discovered does not work. You can get a stand alone cross over like the dbx DriveRack and fix the problem. Then down the line add a second sub and you will be in business. 
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!!