Look at the label on the drives. They should say Master, Slave, or Cable select. The jumper should match the position of the IDE cable (end of the cable is master, middle is slave). The main drive is the master, the secondary drive is the slave.
How do I set the jumpers though?
SATA or IDE? SATA drives dont have jumpers for Master/Slave. One drive per cable only.
IDE drives should be marked on the underside or on the label on which pins are what.