Ok first of all make sure you buy a drive that is compatable with your system be it a SATA drive or a IDE drive
How i would go about it would be to disconnect your second drive and install the new drive, enable it and formatt it in either disk managment or a third party management tool such as partition magic 8 or a free program like Parition logic (
LOOK HERE )
Once you have the drive showing up in "my computer" I would then use a clonning program such as
XXCLONE to copy the contents of your old drive over to the new one, make sure you have a read of this great tutorial that will help you ensure the clone drive is bootable
LOOK HERE
once you have done that i would then disconnect the old drive and then reconnect the drive you want to keep out of the 2 old ones, be it the first one you disconnect or not, boot into the bios and then make sure the new drive is second in the boot order after your CD/DVD rom, save and exit then your set