Yes, I believe in the biamp setup, that the 500 is underpowered relative to the 1kw, with the crossover at 200hz.
For 'average' music, the 50:50 point is about 350hz. So, with an even lower crossover it may be 45:55 or perhaps worse.
I'd start by using same amps on the 2 sections....
Now, I'd also measure power output to the panels, even as crude as a DVM. I think the power rails in those amps is what.....80 or 85 volts?
Have you popped a fuse.....yet?
The noise you hear is mylar slap, basically the panel 'bottoming out'. Not recommended, as a general rule.
I don't know that 20.1s play much/any louder. Just move more air and so can couple to a larger room. The NEW 3.7s may have better frequency balance or sound better to whats left of your ears.
If you got the loot to just toss out that you may 'need to upgrade to the 20.1s.....' I'd suggest taking the cash and up-amping to a brace of Pass amps. Don't get me wrong, I, too, have a 'd' amp. And while I'd love to have the pass INT-150, I'm sticking where I'm at and will do room tuning before turning to the bottomless pit of bi/tri amping with the thousands of adjustments.
Keep us posted on your progress.