You've got a couple options.
Assuming your drives are ATA-66 or faster, and you are using an ATA-66 (80 wire) cable... the one with a blue connector at one end...
The master drive must occupy the connector at the terminal end away from the blue (motherboard) connector end, and the slave must occupy the connector in the middle. Most of the time, you can set the jumpers on both drives to "CS" (cable select) and the terminal drive will be your master. Optionally, using jumpers, you can set the terminal-connected drive to "master," and the other drive (attached to the middle connector) as "slave."
Once you've done this, at next boot, go into BIOS and confirm which drive is master (usually denoted IDE-0) and which is slave (usually IDE-1)... sometimes these will be IDE-1 and IDE-2, respectively.
You can now proceed with partitoning and formatting as you decide.
PS: Hope you didn't toast your original drive by "hot plugging" in the second hard drive!