I don't think that the BIOS update will help (though it isn't necessarily a bad idea, if there's an improved version available). The only thing I could see wrong with the BIOS is if SMP mode is disabled—there should be a manual on the Supermicro website describing how to enable it, if it can be changed. (With some really old motherboards, it's controlled by a jumper, but I'd suspect it's a BIOS item on this board—maybe something like "Enable CPU 1" or "Enable SMP".)
Your problem seems to be with Windows alone; in this case, using the CD (or at least the set of appropriate files) seems like the only reasonable way of doing this. Interestingly enough, it is
not illegal to use a copied Windows CD for this (or practically any other) purpose, provided that you own a licence for
that copy of Windows (e.g. if it was included with the computer, but you received no installation media).
Here's the appropriate instructional resource from Microsoft, detailling the procedure. It's written for Windows 2000, but should apply equally to any NT 5 variant.
And, since you mention that you couldn't select the right HAL, in Device Manager, did you select "Show all hardware of this device class" in the Update Device Driver Wizard? See the attachment for what I mean.