One reason for removing the first original HDD while you partition the new one is that FDISK, if it sees an active partition, won't let you make any other partion active and doesn't provide any method (short of deleting the partition) to deactivate an active partition. [Ranish Partition Manager (free) will let you deactivate an active partition]
You tell the BIOS which partition to boot from and so it actually doesn't matter if you have two drives both with an active partition.