Depends on what you are after. SATA drives always have to be on separate channels - there is no Master/Slave relationship. If you want to RAID 2 drives - you basically have two choices. RAID 0 (Striping) and RAID 1 (Mirroring.)
RAID 0 spreads the data equally over two drives, and doubles your capacity. RAID 1 duplicates the drives - the system sees one drive, but if one goes sbad,the other works and you lose nothing. With RAID 0, if EITHER drive failes, you lose everything.
Correct your understanding - each group of 2 ports can create one RAID array. Example, my current RAID PCI card has 4 ports. Port/channel 1 and 2 are my data RAID 1 array. Port/Channel 3 is connected to an external SATA drive - not RAIDed.
My boot drive is a single PATA/IDE drive - not RAIDed.
There are also SATA PCI cards with 4 ports that are not RAID cards. Each port is a separate channel, and can support a separate SATA drive.