Does the motherboard control the disk drives?
Does the motherboard control the disk drives or does a adapter card control the disk drives?
Normally the motherboard interfaces with the disk drives through onboard controllers that are controlled by the southbridge chip found as standard on motherboards. These controllers are generally either PATA or SATA. An adaptor can control disk drives but it would have to be installed and configured with the correct drivers during the OS install. An adaptor can be PATA SATA or SCSI depending on the type. There are new SSD based cards that can interface through PCI express but these are far from common at the stage. It is possible to have multiple types of controllers running at the same time. The most common interface is SATA these days. RAID can be onboard depending on the board or added by virtue of a controller that supports RAID. Some adaptors also offer ESATA but often allow either ESATA or SATA but not both.