You shouldn't really have a problem. Most modern motherboards support USB at a low level.
If you look in the BIOS do you see a option like USB Dos Support (or something similar)? If so, just enable it. If you don't see that option, check you have the latest BIOS version.
My secondary machine (an old Athlon Slot A with an Asus K7V KX133 mobo) is running with a USB keyboard just fine. My main machine (Athlon 1.4 with K7AMA mobo) is running with a USB Intellimouse. Both machines are able to access the USB devices from DOS.