@Derek Duncan: Firstly, make sure your subs are in the best location for sound that aesthetics will allow. Put your AVR into Direct mode, put a sub in your chair, and crawl around the room where you could reasonably leave each sub, listening for bass sound quality with familiar music.
Once you get the subs where you want them, if they sound muted in some frequencies they could be cancelling each other out. Try setting the phase of one of them to 90° and see if it helps.
Now, run Audyssey setup. Upon running setup, our Marantz AVR initially sets the LFE level very conservatively. You'll probably need to turn up the subwoofer channel in the AVR by at least 7dB, maybe more. Definitely salt to taste.
Also, make sure Dynamic EQ is turned On. That will make a significant difference in the sound. For Dynamic Volume, I recommend either Off or Low. Play with it and see which you prefer.
I recommend setting the surround mode to Auto. You can do this either by hitting the Direct button on the remote multiple times cycling through Direct -> Pure Direct -> Auto; or by using the Android or iOS app, or the web interface.
For a more comprehensive guide to Audyssey setup,
see this AVS Forum post.
P.S. When you decide your Klipsch and JBL subs aren't cutting it, ask us for advice on something a little more worthwhile. More often than not, you're doing yourself more harm than good by matching the brand of the subs with the brand of the mains. Internet Direct subwoofer companies will offer much better bang for your buck. I'd also recommend some sort of bass management, but there's only so much a pair of 10" Klipsch subs can be polished.