If you can get to the disk administration tool (I'm asssuming you're in WinXP or 2K/NT) you should be able to locate the physical disk and see what kind of partitions it has on it.
WARNING: If you have data on the disk, DO NOT reformat to access the disk. Use a Knoppix LiveCD or similar tool that will access the existing partition and copy your data over to the first HD or to CDs first.
Then repartition the second HD and format it as NTFS or FAT32 or whatever you want to use...