If it's been formatted it doesn't matter. But make sure your jumpers are set correctly; you have two choices: you either need to set both for Cable Select (CS), or (generally preferred) set the Master drive (the drive with the OS) to Master (MA) and the Slave drive (your storage drive) set to Slave (SL).
In either configuration, the Master drive should be connected to the end of the cable, and the slave at the center connector.