It really shouldn't be a problem. I do it all the time. Just let Windows load up generic drivers for all the new mobo components. This should take quite a while and you may think that Windows has crashed but it shouldn't. Then when Windows finally loads up, pop in the CD that came with your mobo and load up all the necessary drivers.
I have heard of people who have had difficulties, but nothing bad has yet to happen to me. I have an old 10G hard drive that I use to test things. This thing has been in and out of at least a dozen different mobos with several different chipsets and it has worked everytime.
To start press any key. Where's the "any" key? --Homer Simpson.