I set up a system at home that has two SATA controllers: one is on the motherboard (nvidia chipset), while the other is on a Silicon Image SATA card that has three eSATA ports. Here is the relevant lspci output: There are two primary drives connected to the onboard controller and four connected to the controller card. One of the primary drives on the onboard controller contains the operating system (Ubuntu, in this case), while the other drive is blank.