Again Linux falls down here in the "ease of use" area.
To tell Linux you are running a USB mouse under XFree86 or Xorg, you need to modify the appropriate lines in your /etc/X11/XF86Config or /etc/X11/xorg.conf files. Generally you'll see a line something like:
Option "Device" "/dev/psaux"
Which tells the system that your mouse lives on the PS/2 port. You need to tell it to search the virtual USB bus instead, which maps itself to /dev/input on newer kernels:
Option "Device" "/dev/input/mice"
X can support as many inputs as you can give it. If you want 8 mouse inputs on your system, then you can configure it as so. Ditto for unlimited numbers of keyboards, video cards, monitors, etc. GNU/Linux substitutes much automagickery with total user customisability. End result is you can do almost anything you like, but you need to do it manually via config files. Greater control, but at the expense of ease-of-use.