If you are doing a clean install of windows, you may want to repartition the drive....
If you do split the Windows partition, you might have trouble with booting Linux... The partition numbers might change, and Linux might not recognize which it needs to mount where.
Take a look at your /etc/fstab file. If it lists partitions like "LABEL=/", then you should be OK. If it lists them like /dev/hda2, then you might have trouble. If there is an extended partition (/dev/hda5), and your Linux partitions are logicals (/dev/hda6), then you should also be OK.