I'm getting kinda muddy low end and I want to try and tweak crossover info if its possible or even an option that I can understand.
The Sony's Speaker Menu is where you define the number of speakers you have, the type (Large or Small), the crossover frequency and the speaker distance. Speakers set to Large will be sent a full-range signal, and speakers set to Small will be sent frequencies from 40Hz - 200Hz and up while the subwoofer will be sent frequencies from 40Hz - 200Hz and down, depending on the crossover frequency setting you choose. The front, center and surround speakers each have their own setting. I believe the default is 120Hz, which is probably too high for your front main JBL E-80.
If you are using the Bose 201 speakers (sitting on top of your front speakers in your photo) simultaneously with your front speakers, that may be contributing to your "muddy low end", as well as providing unwanted acoustical interaction.
And if you are, they would have to be connected either in series or parallel, either of which would present a sub-optimal speaker load to the amplifier. Most budget receivers do not do well with 4 ohm loads (if they are connected in parallel) or produce enough power with 16 ohm loads (if they are connected in series). My advice is to
disconnect them.
Also, having the front speakers too close to wall boundaries can increase bass output, sometimes resulting in the sound being muddy or boomy. If you can't move them out further from the wall, you could try experimenting with pluging the ports. If port plugs were not supplied, "stuff a sock in it".
With an AV Surround Receiver there are many settings that need to be optimized, so I would recommend becoming familiar with the setup as outlined in the owner's manual. If you don't have yours, here is a link to one.
http://a248.e.akamai.net/pix.crutchfield.com/Manuals/158/158STDH800.PDF Good luck!
Steve