Enter Bios and set the boot option to the proper drive before proceeding. As in hook up the drive and go to bios and set the proper drive to boot from. If you don't know how to set this up all the info is in your motherboard manual on how to set up boot order.
Depending on how old your machine is and if you are using SATA drives or IDE drives you might need also to have proper cable order and jumper settings for old computers with IDE drives.
Primary boot drive should be set to master using jumper configuration explained on the side of each HDD, and should be connected to the middle plug from the IDE cable, second should be set to slave from the jumper configuration and hooked to the end plug.