Does Prime95 use multiple cores? (Is there a difference in this regard between running it from Windows, UBCD, or UBCD4Win?)
If it doesn't, are there tools out there that will (preferably via a boot disc)?
Yes Prime95 utilizes multiple cores. Just turn up the 'thread count' option to at least as many cores as you'd like to test.
As long as the OS you choose to run it on sees your multiple cores, Prime95 should use them.
When running a torture test in a recent version of Prime95, the
Number of torture threads to run can be varied. I believe it defaults to the number of CPU cores on the machine.