The Serial ATA bus is point to point, and as such there are no subchannels, so there is no Master/Slave system. In order to be compatible with existing IDE drivers though, SATA emulates PATA.
I think your question stems from a general misunderstanding regarding Master and Slave concept. Technically there is no performance difference between Slave or Master, Primary or Secondary channel, so it doesn't actually matter where your hard drives are connected. However, with PATA/IDE, a channel (Primary or Secondary) runs each device (Master or Slave) at the lowest speed match. In general, there are conventions to follow to ensure best-case performance.
SATA drives will usually end up as logical 3rd Master and Slave and later. Most BIOS have configuration options for compatibility modes that allow SATA drives to occupy Primary or Secondary slots, but this is predominantly unnecessary, and in most circumstances, prevents the use of AHCI mode and associated SATA enhancements.
If you want more information, tell us a little more about your hardware.