If I understand correctly. You got some additional USB ports that attach to your motherboard via a ribbon, and screw into an open space on the back of your case, right? wrong?
If you have a need for more than two USB ports than sure, hooked it up.
It's a new motherboard, so possibly any ill effects you were having before, that made you disable the USB - may no longer be a problem. Give it a shot, mayb it will work fine. If not, then just disable it in the BIOS like before.