If the puzzle mats don't help, then the Manduka plyo mat (which is just a thick yoga mat) won't help that much more. I'd be concerned that a second layer of puzzle mats would be unstable and slide a bit.
How much "noise" are we talking about? Thuds and thumps? Then you need to work on your technique. Instead of going for height at first, go for a soft landing. Think of jumping up and landing like a cat, very softly, like you're landing on a glass floor that will break if you land too hard. Also, be sure you are landing toe-ball-heel and not flat-footed, and cushion the impact by bending your knees when you land, which will allow the muscles to absorb the impact instead of sending it into the joints. It just takes practice to get the technique down and train those muscles.
If all else fails, you might want to consider getting a rebounder (mini-trampoline) that you can take the moves to. Also,
www.power-systems.com sells plyo boards that are basically plywood squares with foam padding on the top and foam feet that cushion the blow. (If you look carefully at Cathe and the gang in the KickMax high impact section, their floor seems to give a bit, which would be similar to the cushioning effect of these surfaces).