As Liam says boot from the DVD to launch Windows Setup. When it asks you "What type of installation do you want?" choose "Custom". Select the partition you want to install to, click "Drive options", choose "Format" and acknowledge the warning, then click "Next" and the installation will begin.
You won't necessarily have to re-install every bit of software you have installed to separate partitions. Some will rely on components installed to C: or registry information, requiring a re-install to work again, some won't, some may recreate the bits they need automatically (like Steam), it'll depend entirely on the application.