if you just built a pc you can either install the drivers from th cd provided after installing windows or downloading the latest from the motherboard manufacture.
if you are replacing the motherboard you will need to reinstall windows if the motherboard is not exactly the same.
in youre case you say that you are swapping from atx to matx if i understood corectly.
in this case you can first test if it works.but best of is to do a clean install.