it is recommended to do the repair install. when windows loads, it loads drivers for the specifics of what is in the system, so motherboard specific things could be using different drivers, and cause windows to freak out. especially since you are going to a whole different type of setup, from intel to amd. completely different chipsets.
when you set the system up, after you set everything in the bios correctly, set your boot order to CD, then hdd.
restart with the windows installation CD in the drive, and when it gives you the option for repair install, choose that. after your done with that, be sure to install your motherboard drivers, which should have come on a disc with the mobo. better yet, download the latest drivers from the website.
back up any critical data from that drive first, just in case something unexpected happens.
even if something truly bizarre happened, worst case scenario is you buy a new drive, do a clean install onto that, then install your old drive as a secondary and move your files over from it.
its not likely to be an issue at all, just better to make sure you wont risk losing anything important.
any questions or problems, let us know, we'll help you out!