If you want to change stripe size - use raid controller configuration/management utility provided by firmware. It's require an array recreation/reformat and can not be done using gparted or any other similar tool.
Partitions on supported drive media (are you sure your controller is supported by W2K3? otherwise you'll need a floppy with driver ad floppy drive itself for sure) can be created during Windows Server installation on early steps. You can create both partitions for OS and Data here (or create partition only for OS, install OS, then create Data partition using Disk Management snap-in later).
But I'm sure partitions created using with gparted will be the same as created using any appropriate software (Acronis, Paragon, etc) except NTFS cluster size. If you care about THAT (not RAID stripe size as specified in ori. question) - use gparted as it allows to specify NTFS cluser size while formatting NTFS partition. W2K3 installer will create NTFS partitions with 4K NTFS cluster size for partitions up to 16TB (http://support.microsoft.com/kb/140365)