I placed a half-inch divider on top of the sub-woofer, which then carries the PS3.
No spaces between then besides the wood I used to divide them.
The bass knob on the X540 control pad is set to around 1/3 so not that much bass. As for magnetic shielding, I have no idea. There is no way to suspend that divider. I could maybe place another half-inch wood in between but thats about it.
I would have to buy a longer HDMI cable so I could put the PS3 elsewhere.
Other threads mention that the magnets and vibrations are the probelm but maybe they were talking about those big bad sub-woofers not something like what I have(smaller, weaker, doesnt shake as much LOL).