Installing a new MB isn't too tricky. Keep in mind if it's a different make and model from the one you have presently, you will need to load the driver and chipset files from the CD supplied with the board. I haven't done many swaps of MB on systems, just built new systems with new MB and harddrives, so it was a clean install from scratch. If you are reusing a drive, it might be easier to do a clean install of your OS after swapping the MB.
Just a thought.