No, do not reformat before you install the new motherboard.
Install the board, and if you keep crashing to the blue screen in windows, THEN reformat. For example, I have had friends that have upgraded just the motherboard to a different model of the same brand, while I upgraded from an ECS with an ATI chipset to an eVGA with a Nforce chipset, so windows was REALLY confused.
My other suggestion: Have you already bought the board yet? If so, congratulations on your new mobo, but if not, I suggest well, anything but ECS. From my experience, their customer support and construction quality absolutely suck, especially when you can get comparable boards for the same price.
Hope I was able to help you out.