You will need to reformat the drive to the mac format first. Time Machine can't work with NTFS or FAT32 formatted drives. If you want to use the whole disk, just use disk utility and use the erase function and specify the format to be "Mac OSX Extended." If you want two partitions, go into "Partition" and select a 2 partition drive scheme, set the sizes and formats you want each partition to be in, and hit partition.
After that, just go into time machine and set up the partition you want as the new backup disk. At first, Time Machine will back up all the files on your computer, which will take a while. After the first back up, all subsequent back ups will only be of changed files. I would recommend having a Time Machine drive at least twice the size of your internal drive, so that Time Machine has enough room to keep backups for a longer period of time. When the drive fills up, it will start deleting old backups to make room for the new ones. The more space you have, the longer the backups can go back in time.