What type of connectors do these HDD's have ? ?
If SATA put the new drive on one of the 1st 2 MBoard SATA connectors...
Some boards it'll be 1 and 2...some will be 0 and 1.
Then move the old drive to SATA 3 or higher...this will stop the BIOS from trying to boot the old drive...you can then format it and use it for storage.
If they are IDE the new drive should be jumpered as master/master w. slave...and the old one as slave...then connect them accordingly...
MB=====================slave=====master.
You can then enter the BIOS at boot and set the new HDD as 1st boot priority in the advanced options menu...press F10 to "save changes and exit" and the PC will re-boot.