Okay, not sure if I'm off base or anything here, but here's my take on it:
Puppet- not sure how you're planning on using this new sub or whatever, but bear in mind, that your Z560 sub is not just a sub... It's the whole "brain" for your Z560 speaker setup. Unless yours is different from mine, your computer outputs (the dual mini plug for front/rear) goes into the control pod, then terminates in a ps/2 like plug that gets plugged into the subwoofer. From there, the signal gets split up into the various channels that then goes into your 4 speakers. So if you blow your sub, you're going to have to find some way to either replace the driver in the existing sub housing, or rewire it to an external sub. Your sub is also where all the power to your satellites is coming from.
So you can't just make a sub and somehow hook it up because there's nowhere to hook it in (no specific sub output)... Not unless you use an actual receiver and hook up the speakers. Of course, the other thing you can do, if you're a real basshead, is to ditch the four satellite speakers, and get some bookshelf speakers that have extended response into the bass regions, and hook those up.. That's the beauty of the 560's IMO, the ability to replace the satellites with something else.
As for the Z560's, if your sub blows, I'm sure you can get something comparable through Logitech. When I first got mine, one of the speakers started sounding funny. I called it in to Logitech, and they told me that they were having some Q/A problems with the sub, and that they would send me a new one. Rather than sending mine in to them, all they wanted me to do was to cut off the power cord to the sub, and then send that in along with the control pod. Then they sent me a whole new speaker set. This was maybe a year and a half ago or whenever. So now I have 7 good satellites, 1 sub, and another perfectly good sub that's missing the plug from the power cord... I guess if my sub ever blows, which is not likely, then I'm sure I can just splice a power cord, or reterminate the power cord onto the original sub, and have another perfectly good sub.
Hope this helps..