For the best performance with the least amount of windows errors a clean install is always preferred, however you can boot up in safe mode and install the new drivers off the motherboard disk and take your chances. If it doesn't work you can then do a clean install. I usually put windows in its own partition so i can do a clean install with out having to reload all my games.
If you have an OEM copy of Windows, you can't technically install it with a different motherboard than it was registered with. If it fails to register with MS you can call the number and plead your case to a human. Some win, some lose.