assuming windows autodetect gets enough out of your new mobo to get you into windows, re-installing it is not really necessary, simply install all of the drivers associated with your new one, (eg, bios updating software, raid drivers, and other things like that). Once that is completed, find your old mobo under your hardware profile:
right click my comp, properties, hardware tab, device manager.
and uninstall the drivers and components associated with it (NOTE make sure they only apply to your old one, and not the new mobo) This will remove any use of the old one and leave your new motherboard in it's place.
It isn't a huge deal to swap it out, but do be careful with the parts as you are making the switch as they are static sensitive. Also buy a good quality thermal paste such as arctic silver to put your processor back in
