If you're planning on formatting, only format the drive where windows is installed (C: probably). There's no need to format non-system partitions.
Just be extra careful when reinstalling that you only format the system partition and install to there. Of course, any and all data on your formatted drive will be lost, so you might want to move all personal data to your other partition.
You might also want to resize the partitions before hand so that your Data drive has more space than your system drive. I would leave about 30 gigs on System, and then give the rest to your data partition.