"primary" and "secondary" refer to the channels themselves, that is, the connector if you dont know what a channel is. "master" and "slave" refer to drives on a channel. you dont set your drives to "primary" or "secondary" but you do set your drives to "master" and "slave". this also corresponds to the motherboard channels. what connector of the controller you plug your drive into dictates whether or not the drive is in the primary or secondary channel.
so, if you have 4 drives on the card, you would have the following:
primary master (a drive connected to the primary channel, with jumpers set to master)
primary slave (a drive connected to the primary channel, with jumpers set to slave)
secondary master (a drive connected to the secondary channel, with jumpers set to master)
secondary slave (a drive connected to the secondary channel, with jumpers set to slave)
you can have your drives in any order you want, but the standard is to have the HDD on primary, and CD\DVD drives on secondary. if you're using your promise card and the motherboard's controller, i recommend putting the optical drives on the motherboard.