Motioninjoy supports connecting a PS3 controller through the use of a blue tooth dongle (as long as it has EDR support I believe). Unfortunately it is not possible to do it with multiple ones but you could probably do it with one wired and the other wireless.
Oh and I've never used PCSX2 so I'm not sure. I guess it depends on it's controller plugin. Most emulators I've used (such as project 64 using n-rage input plugin) support controllers fine. (btw betterds3 is an alternative to motioninjoy after you install the drivers needed for the controller)
MotionJoy has an explicit mode for compatibility with PCSX2, the only question is the multiple controllers. Via two cables I'm pretty sure thats easily possible, both via bluetooth I am not sure but cant think of any reason why not.
I remember reading in the FAQ (the main site is down for some reason so I can't go look) that only one bluetooth dongle can be plugged into the computer and no other bluetooth devices can be used besides the controller itself. Although the wording didn't imply that you couldn't run multiple controllers at once on the same adapter now that I think about it. It may actually be possible to do so.
That's pretty much a basic tutorial for how to set it up with bluetooth. It seems that you can do it with two controllers. Just check to see if your dongle has EDR support otherwise it won't work. This is the dongle I happen to use myself.