You can run Windows 98 on a Dual Core machine, the but it will only be able to use one core/processor (it doesn't have multi processor support) so it will be a waste.
Another problem Win98 might encounter is not recognizing the motherboard chipset or the drive controllers (if you have SATA disk controller), which will give you lot of grief.
Same with freeDOS, you can run it, but it will only utilize one core.
(why the hell are you trying to put Windows 98? This is asking for unwanted pain)