Windows should be installed on NTFS.
Backtrack should be installed on EXT3 if the drive is a hard drive (not SSD) or EXT2 if the drive is a flash drive a SSD.
The data partition should be fat32. You could use NTFS and backtrack can read and write to NTFS using the NTFS-3G driver but I have had minor issues writing to a NTFS partition from inside BT. I have never had a problem reading or writing to a fat32 partition.