USB has 4 pins - two for power (gnd + some line for volatge & current) plus two lines for data (data+ and data-), data is sent in a differential stream using a bunch of encoding stuff we don't need to worry about for this.
my USB ports on my main board work fine, but then so do the ones that have a cable attached to the ones taht are on my mb. do you have an extra USB board ? if so i would go with the ones onboard the MB.
when you get it hooked up and you issue a usbview then at a minimum and unknown device should show up in the usbview window.