I have the UD3R board, and it works fine with my one-size-fits-all USB motherboard connector coming from my case (tested them all with a USB flash stick to make sure).
I'd say test the ports by sticking an old (preferably cheap) USB flash disk or other comparatively cheap piece of hardware (I have an old 32MB drive that I repaired for just this purpose).
One pointer that I have for you, however, is make the connections before installing PCI and PCI-E cards. It'll make life a whole lot simpler, and you'll actually be able to see what you're doing. While this may seem like a no-brainer, you would be surprised how many times I have either forgotten to do it or was lazy and unwilling to do it.