I don't see this being a problem as you have to connect your controller to your PS3 for the system to recognize it before you can use it. However, if you plugged the same controller into both systems so both systems recognize it, something may happen. Try it out and let me know sometime! =)
When your register it with a PS3, it will only work with that PS3, and then when you register with another one, it wipes the other machine off. The same happens with the wii.