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 am not sure about  Polk but I had a NHT sub years ago that only sounded right if wired amp to sub to main speakers and you set the crossover on the sub. 
ubee, your problem is that you are not using a high pass filter in front of your amplifier. You need to get the bass out of your main speakers. The PSW 550 does not have a high pass filter in it's cross over. I believe your integrated has a preamp output and a direct amp input. You could use an outboard cross over in a loop using the preamp out/amp input. You would then disable the crossover in the subwoofer. The only other way to deal with this would be to put an appropriately sized capacitor in series with the woofers in your main speakers to roll them off at 6 dB/oct. 
I am not sure how to improve this situation. 
Easy: new speakers. Your bookshelf speakers are max'd out. 

Your amp has tone controls so what you might try short term is turn the bass down. Your little speakers can't handle it. Then turn the sub up to compensate. 

Its a crap solution but all there is without better speakers, since fundamentally your problem is nothing to do with the speakers its you. Play them within the range they are intended for, or buy ones designed to play within the range you want.
I looked up your sub you need to wire like the manual says and set the crossover and volume on the sub.
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!!
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. 
As mijostyn suggested, add a 300uF capacitor in series with your main speakers to roll off low bass at 6 dB/oct.

Or use a high pass filter in series with your main speakers to roll off low bass at 12 dB/oct.